Which version of RTR did you play?
Honestly, I enjoy commanding phalanx armies, even against the Romans. The trick is to keep your line in two sections and have a reserve you can run up the middle. I've noticed that the AI tends to split its army in half to flank me, at which point I simply pivot my flanks and use my more mobile infantry (usually thureophoroi, Galatians, Cyrtians, or some other reasonably well-armed locals) to cover the ends. Here's an early version of that strategy I uploaded awhile back:
The trick is to follow Alexander's lead and have some heavy cavalry on hand. If the Diadochi had kept their heavy cavalry arms in better condition, Rome might've had more trouble with them. A good heavy cavalry arm can exploit any attempts to flank you by defeating the enemy cavalry in detail and then steamrolling their infantry. (I like to keep some hypaspists around, too, since they can fight off any enemy cavalry while my main group is gone.)
Otherwise, I, too, prefer a united Rome. The three house idea was intriguing, but just not historically accurate. Here's my favorite method for using the Polybian-era checkerboard formation while still maintaining tactical flexibility:
I find that works pretty well.
(N.B.: All of this is with Sinhuet's AI formations, slightly modified by me and a couple of other people {Darth's are nice, too.}. The normal AI couldn't find its way out of a paper bag with radar and a native guide.)