Of course, the following observation is scenario-specific, but in the case of Red Thunder 88, it's probably better to take command of both 3rd Shock and 3rd PPR armies, as both are "assigned" the axis of Magdeburg->Hannover->Arnhem or thereabouts.
Otherwise, you end up stepping on the toes of the AI fairly consistently and it seems farcical that units stacked in the same hex wouldn't be able to cooperate and coordinate in some way. I just went ahead and used the 3rd PPR forces by setting the Formation to "Manual". Then, when the attack axes of 3rd Shock and 3rd PPR started to diverge, I handed 3rd PPR back over to Elmer. Pretty cool!
Of course, you could also just edit the 3rd PPR's objects and assign them, say, a slightly more southerly route or something. I find the AI does a surprisingly excellent job on the offensive and actually managed to take Berlin faster than I was able to do. The offensive in the North is likewise being handled well. Notably, Elmer doesn't make the mistake of over-extending his forces (leaving them ripe for local counterattacks and then going into Reorg) nearly as often as I seem to. Elmer must not be as ambitious ;). He also taught me to launch artillery and airstrikes *before* going in on the assault. Maybe that's why he gets better results?
Anyway, 3.4 is really great. Can't wait to see if they expand on this "part-AI" way of playing in 3.5. It really is a lot of fun and feels more authentic somehow. I could easily see a version of TOAW that used this method of setting objectives for formations exclusively, but the UI would need a bit more polish, I think, to make it seem like less of an "add-on".
Call it "The Operational Art of Elmer" ;)