Haven't played one in a while but was a big fan of the following: Command & Conquer (original) Age of Empires 2 Total Annihilation Dune 2 Any recommendations?
There are quiet a few good ones out there. Autumn Dinasty Starfront Also Command and Conquer If you're willing to learn a complete new way to play these games on ios you should check out red conquest. Unfortunatly it's not universal but defenetly worth a try.
Amoebattle is awesome if a little different, but it does a great twist on the genre to make it work on a touch device Blue Libra series is also pretty good if you are into space battles. Autumn Dynasty is a great game with a good degree of challenge to it. Land Air Sea Warfare is supposedly good, though I don't own it. Warfare Incorporated is good if you don't mind heavy emphasis on online play. Falcon Fusion, while more if a real time RISK sorta RTS, is very good as well. The settlers is also very good IMO, though some disliked it, I liked it for trying to stay to its roots with equal emphasis on building infrastructure and warfare. Then there's Red Conquest, which was good. Oh, almost forgot Robocalypse as well, though I don't play it much... iPad owner who loves his universal and all! Also I second Eufloria, Star front: Collision, Command & Conquer: Red Alert, even if the last one got bad reviews!
The best I can describe it is that it is a relaxed RTS. There is strategy, but you don't have to worry about tank rush TA tics and such and can play at your own pace but a more tactical and less reactive level. I love it, but it can be very abstract looking if you have no context of what you are seeing. After leaning to play though, you will find a beautiful and fun RTS. Check out this gameplay review if you are on the fence: http://www.youtube.com/watch?v=Y0JiMJCJ8aU And this one, though of the PC version, and barring the guy being a Twinkie who can't be bothered to read the in game description telling him they are plants, calling them birds and animals, gives a good overview of the gameplay: http://www.youtube.com/watch?v=_XtP6HzAEvs