I saw an interesting idea in Pax Imperia:Immenent Domain. It was more like interplanetary war than OP2 style, but the way the ships were setup was damn cool. Basically each hull type (combat chasis type for OP2 I guess?) had so much room to pack systems into. You could research the hull types, the weapon types, defensive techs, etc. and then pack whatever would fit into whatever hull types you had available. Each component would of course add to the build cost. So yeah, it allowed for highly customizable units which was a lot of fun. Also, if there is a particular situation you needed to deal with, you could custom tailor a unit to handle it.
The only problem with that idea, is it took a while to design ships, and there wasn't really any way of keeping an eye on the game while you were doing it. I can't imagine taking time out in a real time strategy game to design the units you wanted to build. But maybe if the idea was modified a little so certain defaults were always available (and good ones that people would actually want to use frequently) so designing your own wasn't necessary. Also, it'd be cool if you could design units before game time and just have them stored. Then once you've researched all the techs in the game, it would become available for building.
Probably a little too much work to do something like this, and maybe a little hard to incorporate it into an Outpost style game. (Although, Pax was real-time strategy, just a bit of a slower paced game for the most part.) But hey, it's still a cool idea if you wanted to consider it.
The cargo train idea sounds kinda cool. Although, it'd have to be done so the volume of ore it hauled made up for it's lack of speed. If it moves 3 times slower, it's gonna need to haul more than 3 times the ore to make it worth while to use one.
I don't think I much like the idea of cloakable units. Granted, I had some fun with them in C&C, but I'm not so sure they'd fit well with Outpost2. Maybe if you went with something like camaflouged units instead? Kinda like the cammo pillboxes in C&C Red Alert. You could see them if you were really looking for them, but they didn't appear on the mini map and were hard for your opponents to see on the main view.
Oh, and what about turrets embedded in cliff walls? Make them have a limited arc they could rotate around limiting their angle of fire based on the orientation of the cliff. You could also limit the elevation they could aim at, so they would be useless against targets that were too close. They'd be useful for doing damaged to heavy armoured vehicles approaching, but onces they got in too close, the turrets would be useless. I guess I've always just been a little dissapointed with how weak the GPs in OP2 were.