Bloons 5 sucks you in with a huge variety of cute towers, and lots of upgrades. The ios version never took off, but Gemcraft is a port of a hugely popular flash td. I enjoyed it a lot. I find most of them samey samey so I'm not the best person to ask...
In the order that they popped into my head: iBomber Defenseacific, Four Days: World Dense, Tower Defense HD, Guns n' Glory (both of them), Jelly Defense, Starfall... Also check out Anomaly Warzone Earth. It's a reverse tower defense game where you're the attacker. One of the best iOS games ever made.
Cubemen is worth a try for something different (has a level creator too) but if you want to go more down the true RTS route try Autumn Dynasty. Beautiful but very hard game!
Forgot about Cubemen, great game. As far as RTS games go, Land Air Sea Warfare is the gold standard for me. I still play at least one skirmish a day after all this time. I really like Starfront: Collision too. Edit: Heavy Mach Defense is another great defense game.
OK then. Well, we will have our first TD game ready soon, so you can help us beta test if you want and tell us if its good or not edit: hmm, dunno why I quoted myself there! Obviously that was a reply to bramble
Elf Defense and Lich Defense by Jelly Oasis are ones that I'ved enjoyed and periodically play, though they are a bit grindy.