Hi,
Some of the things in this post may sound like I'm thrashing the game, so first I want to say that this is THE game for me; I was so happy to see it available for the iphone. I love it and play every day. I got into authoring missions because I played all of the available ones.
These may be repeats of some of the suggestions posted by other users, I hope they will count as reinforcement.
1. Stop / Hold command; that's a super must, it runes the fun.
2. Unit groups, guard area, guard unit, patrol, follow, all basic functions...
3. Rally point. Having the ability to build units and have them go to a user defined point on the map as soon as they come out.
4. Show trouble. Thank you for the nice voice repeating 'miner under attack', 'base't under attack', even the nice shooting sounds. How about a button that we click and it goes there (or cycles the trouble spots), or maybe some free aspirin

5. Auto repair. Make it that this can be turned on or off during game play and give a way to set at what % health it should kick in. You can still let mission authors disable it from the mission editor (set to player defined, on or off).
6. Building upgrades. Like increase the range of towers, more armor to buildings, power generators generate more, warehouses hold more... Make some use of that research center.
7. Andy. Please allow to build Andys in the HRC
8. Upgrades to units. Better armor, faster fire rate, ability to self repair, invisibility (like invisible raiders for example, and only towers can detect them, or like invisible Andy that we only see when attacking).
9. Flying units. How about build an airport and let some planes and helicopters buzz around...
10. Queue buildings. Just like 10 units can be ordered at a time, there should be a way to order up to 10 buildings in a build queue...
11. Better graphics. Retrographics is what we call this. It's 2009 not 1999.
12. A self-defense function is badly needed. What I mean is if a unit is attacking a building and another unit attacks it, it will continue to attack the building whereas it should stop and attack the unit that is attacking it. If multiple units are present, they should all stop attacking the buildings and defend.
13. Search unit. Sometimes I lose Andy, if he's standing on minerals, it's hard to see him; or some times I need to search if there are bullpups in active. There should be a button that cycles the view between all the areas that contain units (could be the same button as show trouble #4, red when go to trouble, green when cycle units...)
14. Target preference. Allow to set the target priority when attacking so a liberator can be set to attack infantry and hydra to vehicles for example.
It's my understanding from some of the posts that much is held back due to backwards compatibility issues. Although I'm sympathetic to your issues, maybe it's time to say bye bye to the old, low memory PDA devices. Not upgrading is only delaying the inevitable; how long can you do that for? I had this game 4 or 5 years ago on a Windows PDA, this is the still the same game. There has to be more new devices out there than those old clunky ones, no?
This is a great game, it's a shame it does not have the upgrades it deserves.
If you make a new and improved iphone version; I will be happy to buy it again.