I've tried GGPO and Supercade and they have common problems. I'll try to explain what happens to me on GGPO.
1. Sometimes you start/change to "Lost Connection". There isn't any "retry" button. So you have to close ggpo.exe and open it again (sometimes up to 5-6 times until you are logged in successfuly).
2. Sometimes during a game, you lost connection, so nobody can see you after that,. You need to close ggpo.exe and run it again.
3. Although it uses different ports, its system is closer to classic Kaillera, where you had to choose a Server first (in this case, Kaillera P2P could solve the situation, making private sessions and direct connections).
4. Sometimes yo can't challenge someone because he's there, but appears as "Not Registered", so that person has to close and run ggpo.exe again.
5. Interface is good, but went quite bad on the latest versions. That thing they added to userlist where you see "player1 vs. player2" and just below "player2 vs. player1" is just unnecessary; always the first name is the player1 and always that user is the hoster. In addition it moved them to a separated area at the top of the list (similar to Arcade Live).
6. From that point, after starting a match, on Game window seeing "user1 (Player 1) vs. user2 (player2) is unnecessary also. Seeing "user 1 vs. user2" would be enough (the thing is this hides wins/hiscores/time and all the things we are use to get information from.
7. Again, from GGPO client, sometimes you can't start a game even when accepted and ROMset is loaded (ggpofba.exe got freezed after that) .
8. GGPO client uses old FBA drivers, this includes NEO-GEO BIOS, and the supported gamelist in general.
9. We have just an old version of the GGPO source code, which doesn't make me feel so confident about the future of that project as it is shown today.
10. Although GGPO is for free, it needs money to survive... but it hasn't been maintained for a very long time, making ideas about "pay or get this as is today" (or perhaps worse).
11. Isn't possible to use external plugins to add extra features to network's experience (FBA allows that, so we can record online matches, etc).
12. Although ggpofba.exe allows you to select ROM directories, GGPO client needs a fixed path to show gamelist, that can't be changed, so yo have to add your ROMsets to GGPO\ROMs or add at least dummis to avoid this situation.
13. On the best situations, GGPO and Supercade show more lagging that other clients such as Arcade Live (ArcLive). This could mean there's something its staff is leaving out, but as you can see, GGPO forums are almost dead, just users reply users, no staff anywhere.
14. Is always better to have new ideas/receive new projects, than being dependent of "one voice as a mandatory".
This isn't something "to show my hatred against GGPO", is just I "feel" GGPO could die as it is now, Supercade is almost walking on the same way.
Unfortunately that's because seems to be there isn't someone who were working on that project, and... why not, they use the same "method" for online gaming which doesn't sound so "alternative".
Arcade Live shows interesting features (even being so basic), the thing here is "an alternative exist" and "an alternative should exist".
Well... for me GGPO is not so "lovely", so I applaud these new ideas which could improve online gaming experience in those clients (or a new one).