Here's just a list of things that could make the store and forums a better place to browse/visit:
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Please add an edit function to the forums :)
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Regarding copy protection and game DLs: I don't know the current policy for game DLs on JAST USA's store, but all of the games' installers should be updated to the latest version without any old forms of DRM. While I understand that old updates will/should be hosted for those with old package versions so that they can enjoy their games DRM-free as well, ALL games DLed from this new site should not require ANY patches as ANY and ALL patches should be automatically added to the main installer whenever a new patch is released. If this takes too much time/hassle on your end, then the main installer should include all past patches after a certain (hopefully small) period of time has passed from the last patch for the game being released.
- Ranking games on the store: Adding a ranking for all the titles on the store (bestsellers on the top, worst sellers on the bottom) akin to rankings seen on GOG.com and Steam would be really cool to see how well each of the titles is selling compared to other titles on the store - even if exact number of sales are not displayed.
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Tweaking the Game Pages: While perhaps not pertaining to some titles currently available, there should be a list of all the "digital goodies" that a given release comes with (manual, map of gameworld, full/sample soundtrack in FLAC/MP3/other). Also, the system requirements for each game really should be listed - what operating system a game works on is really important (though I'm guessing all the games you sell right now are for Windows only?). How large the game is (in MB if smaller than a GB), what languages it includes (maybe you might consider selling JPN or other language versions of games alongside the ENG localized versions in the future?), links to other games in the series (for instance, on the Aselia the Eternal page linking to Seinarukana and vice versa), and what the game genre/type is directly on the game page. Looking at this game page on GOG.com will give you a good visual idea of what I mean. Of course this website has it's own unique style versus others (and I really like how I can browse the site painlessly using lower-powered devices), but I think that these are essential pieces of information for people looking to buy games from any online store. Also, prominent mention of every game on the site being DRM-free would also be beneficial to those who may be coming from other VN sites thinking that they all employ DRM in their games. I think that this stance should be stated somewhere on each game page (for those games that previously had DRM in their digital or package(?)† versions, you should state that they require the included patch to remove old copy protection).
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Tweaking the "Game Shelf": there should be box art for each game that you own akin to having the game on a real shelf.

†††††††† From the "My Games" tab under my account, each game you own
††††††† should have all of it's related content clearly labelled and organized
††††††† with it. For instance, with your game DL, you should also find the
††††††† "bonus materials" clearly labelled similar to the way GOG.com does it:

†††††††† websites gone for many of these games, you could include all the
†††††††† downloadable content from those sites (avatars, wallpapers, etc.) in ".zip" files. Also, some of the physical versions of games have extras on them that are not available with the DL versions. Even if these are bonuses for those who buy a physical copy, please consider adding some of that content to the games when you buy them through your site (especially the games with OSTs or guides). Any available patches should be accessible from the "My Games" section and not "hidden" at the bottom of each page
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Adding User Reviews, Direct links to support articles/FAQs, etc.: As can be seen in the bottom of the above picture, it would also be advantageous to add the aforementioned features.Being able to see at a glance what problems others are having within one click of the game page of the game they are currently having problems with could save a lot of grief on the support sides of things. Having user reviews would also be a good way for people to gauge the quality of any given title, and would not necessarily need to be done on a 1-5 star scale. Reviews based on what you felt after completing it/while playing it, or some other method might allow people to better see if they would enjoy a specific game or not. Also tags should be an essential feature to the site. While there is a basic genre choice for titles, there should also be specific tags that describe the content of the game in terms of what kind of story it tells, or what kinds of characters it has (of course, avoiding spoilers in the process). A wishlist function may also help supplement forum posts for titles that people are looking forward to the most.
- Site Organization and Exposure: While this new site is a MASSIVE improvement over the previous site, there is still some issues with the way pages are laid out. Things like "Your Questions" [should really be renamed to "FAQs (Frequently Asked Questions)"] and "About Us" should be easily visible at the very top of the page. someone who has no idea who you are will most likely want to know those two things right off the bat. A link to the Dev Blog should also be prominent somewhere to allow people to follow you easier. Most importantly however, there should be somewhere on your main site that shows Upcoming Titles besides tumblr! Ideally, I'd say that it should have a graphic dedicated to it somewhere on the site so that people know you are actively working on projects without having to check other sources to see how far along you are. Ideally, I'd saw whenever progress is made on a game, you should set up an automatic system that also tweets that progress so that those following you on social media can see that you are consistently seeing progress on your games. This would allow people to have more excuses to talk about and bring up JAST USA in different conversations.
- Staying Current and Complete: One of the things I've noticed about JAST USA is that sometimes word about licenses is vague or progress on games seems non-existent even when progress is being made. If you have a license for a game, you should list it somewhere obvious on your site where everyone can see it. If you are working on a game, list it on your Upcoming Titles page! For instance, where it Trample on Schatten, Sumaga, or any of the other titles you've announced but not yet released? If not on the Upcoming Titles page, there should be a dedicated page (that is not exclusively on the forums) that states all the titles you have licensed and where they stand in regards to getting released. You don't need nitty gritty specifics about all of the progress or titles you have licensed, but even a vague, conservative evaluation of where you are in the project and what is holding it back may go a long way in showing how much work you have tackled so far, and how much work is left to go.
- Outreach: I know at this point in time that your hands are tied on releasing Steins;gate on Steam (that's in Mages hands now), but what about your other All-Ages titles in your line up. Off the top of my head I believe there is only one other one - Aselia the Eternal. Why not get permission from Xuse to release the Japanese and English versions of the games on GOG.com? Not only would it be in line with your DRM-free stance, but since the title has strategy gameplay, is All-Ages (so no Japanese censorship laws need to be worried about), and already seems to work on most modern systems, it would open the game to a whole new worldwide market that may not have played the game otherwise. Please consider this idea as I think that title may perform well on the site. While there are few votes right now, it does have a wishlist page there. Also, doing surveys akin to what Mangagamer and Sekai Project have done recently are also very good ways of seeing where a segment of the population stands - post it on the Littlewitch Steam page, your twitter, the forums, and the site - maybe you'll see some interesting results.
(And as a side bar, please release more All Ages titles in the future that are of the same quality of Steins;gate or contain anything related to mystery, cyberpunk, science-fiction, or similar themes. I'm always looking for more PC VNs like that or Aselia the Eternal ^^)