Well the first is for the Dev-Team to decide that, not you -- and secondly, Balance is not an issue when you're just dressing up an already balanced unit with a new model.
You're certainly right that it's for the developers to decide, but that doesn't mean I won't say what I think.
Balance is often oversimplified by people who talk about it. Colours and aesthetics have a considerable impact on balance if they are not approached carefully. For instance, the "earth tones" often camouflage on the mini-map and render you nearly invisible to the less attentive eye. The units may be identicle stats-wise to everyone else's, but they have this special property due to their colours. Anyone who would claim this is not an advantage is just being foolish. Without some system (such as the large icons used in supreme commander) to distinguish "earth tone" colours from the back ground surroundings it's just not practical to allow someone to play with them.
I think you're being way too critical if you think a paper doll insufficiant. I can understand that many features aren't apparent at a higher zoom, but in reality at such zoom you're not going to be able to make out any details anyways. Moreover, I don't think you realize how little option you will get in your system. How many models do you think you'll get for each unit? Suppose there are about twelve (a low-ball guess) units per faction, and there are the four factions. That's around 50 units. Last I checked, it's very not trivial to go through the full range of developing a single unique model, from concept art to the finished product. Even if there are three options per unit (frankly, a paper-doll system will offer far more than that could), that raises the bar to 150 unique models to develop. That's a considerable increase in workload for what is really a very moderate gain. I think you'll get far more variety out of paper doll than you ever could out of entirely different models.