Yeah, shooters on Neo Geo is pretty slim pickings. Strikers 1945 Plus is pretty good, although not the best ever. Aero Fighters 2/3 are decent, but I wouldn't exactly call them great.
I'm confused though. You guys are responding like we're only talking NeoGeo? If you mean all of Kawa-X, you can add 1944 and 19XX as pretty good shooters from the CPS2 catalogue. 1944 is quite a bit better than 19XX, but both are good. 1944 is a very long shooter, though (17+ stages). Get ready for fire-button cramps or save state usage.
CPS2 also has Mars Matrix and Giga Wing - both are excellent
shooters. Must-haves if you like shooters and Xbox emulation.
CPS1 only has 1941, U.N. Squadron and Varth that I'd even begin to recommend. Don't go out of your way for any of the CPS1 shooters.
If you really want to break your thumbs, though, get Varth. It's over 30 stages long and takes well over an hour to complete. (Obscenely long for a shooter, mind you.)
That's it for me, I'm a shooter man.