So I haven't tried everything the new site has to offer, which means this won't be a full list of my concerns, but some things I've been using and I'd like to put forward my feedback, hoping you'll take notice.
1 - Games that were available on the old site are now gone and can't be added to a stack or individually found. One example of this is "Pokémon Mystery Dungeon: Red Rescue Team" which is exclusive to the GBA, yet, it's completely gone. Instead, if you go to the page for "Pokémon Mystery Dungeon: Blue Rescue Team" (which is a DS exclusive), it now says the game is available for DS and GBA... which is false. It does make me think you combined the two games, which is a big problem for people who own both and understand the differences between them.
2 - In the old site, every version of a game had its own page. This was good because some of us have the same game on multiple platforms. Now it's been "dumbified" to only register the game once, listing "alternate platforms" on the sidebar... please, bring back the ability to have platform-specific choices.
3 - In the old site it was already a bit of a pain if I wanted to find "all games" from an old platform, but at least it was an obvious process: select "all games" and then filter by platform. Now, I simply can't find a link to a game list for anything other than "Nintendo", "Playstation", "Xbox" and "PC". Clicking on any of those gives me the option to filter individual consoles from that line but even that doesn't work right, so I'll divide this issue into two.
If I go to "PlayStation" and then select "PlayStation 2 - all games", I still get entries from other consoles which are not the PS2. (non-issue, it's either fixed, or I misread PS3 for PS2)
3.2 - I want to find a list of "all games" for the Sega Dreamcast... how can I do it? Right now, it seems I just can't.
4 - Adding games to stacks doesn't work very well. It gives us 3 options regardless of how many stacks you actually have. A simple drop down menu with all your stacks would be appreciated.
5 - Speaking of stacks, I can create them, but can't sort them. What if I want one of my older stacks to be on top when I visit my stacks page? Just like I can number the games inside the stacks, so they are ordered the way I want, it would be nice to be able to do the same with the stacks themselves.
I'm sure there's more that could be improved on the site, and I have purposely ignored minor things like aesthetic problems (for now) but I'll add more as I find them..