I think they hold up quite well against the GBA titles. I have the specific titles, Final Fight One, Alpha 3, KOF Ex2 Howling Blood, KOF EX Neo Blood, & Guilty Gear X. I find the animation smoother and more fluid in the NGPC than in the KOF for the GBA. The GBA seems to have missing frames. The GBA is more colorful, which is very obvious when comparing the games. The choice is, do you want Chibi characters in your fighter or the traditional realism with detail. I think that the fighters on the NGPC are a lot more fun. If I want portable fighting I go for my NGPC with titles like, The Last Blade, Fatal Fury: First Contact, Samurai Shodown 2, King of Fighters R2, SNK vs Capcom: MOTM, & SNK Gals Fighters. You are not going to get that kind of fun out of the GBA. IMO the fighters on the GBA just don't stack up to the quality of fighters on the NGPC. So, I guess, its Chibi fighters for me.
As for the Metal Slug Advance, I was very disappointed in the GBA offering. It was just not Metal Slug to me. The Metal Slugs for the NGPC are traditional Neo Geo Metal Slug and that is what I like playing.
As for the Sonic game, I don't have Sonic Advance, so I can't compare the two. But the Sonic game on the NGPC is the traditional Sonic that all Sega gamers have enjoyed and loved. It is taken from the first Sonic games. It is fun and plays great even though it is not on a Sega system.
I assure you, that you will not be disappointed in a NGPC.