I agree with you guys that the current choices are very lacking. And some of the disadvantages are really a no brainer. Take all the ones that offer penalties for being IN a city and make you SOV the best army general/adventurer possible. I mean why wouldn't you get the extra points if you plan to never park your SOV in a city?
Of course the reverse is true for the city bonus traits become worthless the larger the map is because then less helpful it is to have that tiny bonus in only 1 of your many cities. Even on the tiny static map in the beta we have had thus far I've never had less then 5 cities and the minor bonus to only one of them was NOT a fair trade off to having my SOV stuck at home.
If anything I think the majority of the SOV bonuses should be empire wide bonuses with possiblably a large extra bonus for actually being in the city. Such as say 10% bonus to all R&D empire wide with 30% or more bonus to the city the SOV is in. I mean because currently a university produces 10 R&D and you can only build 5 in a level 5 city. So that's only an extra 5 points if your parked in the city while you can get the trait the automatically generates 5 R&D regardless of where the SOV is.
i know the above example is in part balance related but even so I can't think of any bonus amount that would really make it worth while. The NEED to level up your SOV is pivaital to the game and thus you must spend much of your time out of the cities. It is especially critical early game when your SOV is your strongest unit and you need to use the SOV to explore and complete quest to help fund your new empire.