Chillingo's Sky Combat and Assault Squadron are the best. They are both almost perfect though on the short side, lenght-wise.
For Your Consideration: iFighter Super Laser: The Alien Fighter Space Invaders Infinity Gene Phoenix Assault Squadron
My collection: Dodonpachi Resurrection (Bullet HELL!) Sky Combat Phoenix (bullet torture) Air Attack Lighting Fighter (Raiden clone) Dodonpachi is simply the best shump out there. Sky Combat has great graphics. The flying sections are good, but no where near intense as Dodonpachi. The vehicle sections are awful. Phoenix has an addicting upgrade system. Air Attack is a solid vertical shooter that doesn't do anything new with vertical shooters. Its 3D graphics just under-par with Sky Combat. Lighting Fighter is again a solid Raiden clone. Nothing too special except the auto-bomb (Dodonpachi has it as well) and special attack feature. Deleted shumps: Super Laser Buster Red Super Laser was simply too obsolete compared to Dodonpachi and others. The 'blocks' in Buster Red from Lv 20+ are major distractions. Deleted.
Top iOS shmups (in order): DoDonPachi Resurrection Espgaluda II Space Miner Blast 1951 World War One (very different, and VERY good) Phoenix Others of interest are Roswell Fighter, Super Blast 2 and Space Invaders: Infinity Gene.
I played Phoenix, Air attack, Lightning fighter on ios, recently been playing Point Blast, really kinda cool but buggy, hope their next update will fix some small issues.