If you take out a single factor of the whole difficulty calculation and emphasize on that, it might seem as if you're punished for e.g. leveling your AW or for purchasing premium expansions. Nonetheless, these things always give you way more benefits than the impact they have.
Thanks that you explained some of the reasoning of the team that led to the current formula for troop size, I guess that will help to give more specific feedback.
First I will give you more details concerning the examples I mentioned in #326 where someone doesn't get enough benefits for the additional costs of the higher troop size.
Let's compare my city at the end of the research tree (actually stopped before troop research) with all expansions available and 433 wonder levels to the city I mentioned above at the end of research and with all expansions as well but many additional wonder levels. The additional wonders are: Endless Excavation, Thrones of the high man, Blooming Trader Guild, Enars Embassy, Elvenar Trade center, Sunset Towers, Lighthouse, Vortex, the 2 chaper 16 wonders and Maze. Furthermore a lot of levels in Crystal lighthouse and Tome of secrets.
In total 153% of my troop size and all the benefit he gets is a bit more mana because of maze and a few drone riders from one of the new wonders. That doesn't only seem as if he is punished, he is punished severly. That was never a problem in the spire, because the rewards he gets there are worth much more than his losses. And since only a very small fraction of all our troops is used in the spire the impact of the higher troop size there is negligible overall.
Concerning space it is simple: t1-t3, supplies and orcs scale more or less linearly with space, but gold (mainly from Abyss and neighbourly help), mana (mainly from Abbey) and troops don't. Therefore at least for people willing to fight manually the troops saved by lower troop size are worth much more than anything that could be built on additional space. And even for traders the space becomes almost worthless once they have enough manufacturies, supplies and orcs to match their mana and/or gold production.
But I guess we have elaborated enough on this problem, I would like to add a few points concerning the goals you mentioned in your post.
You want to give people an incentive to move on in the research tree instead of sitting and simply filling wonders. In my experience cities have paused research for 3 reasons in the past:
1. They wanted to avoid the next troop researches because it was a long way until the advantages of additional research made up for the disadvantages of the troop research. You have handeld this problem quite nicely, simply increasing troop size in a smoother manner with every research instead of troop size research should do the trick.
2. The city was some secondary city for pushing or diamond generation or whatever. Unfortunately balancing is irrelevant in this case.
3. The player was in the process of quitting the game. Again, balancing does not help in this case.
You also mentioned that you do not want to make push accounts more attractive. The most effective form of push account currently is a level 4 city with lots of provinces that are all catered up to round 5 using t1 goods from the main account and returning most of the kp to the main account. These cities only need to produce supplies and gold. With increasing the difficulty of the higher provinces you have possibly made this approach less effective which is good. But scaling troop size with wonder levels and space used actually is very beneficial for this kind of push account. Since the goods needed are provided by the main city it needs much less space than normal cities in the same chapter and since the kp are mainly transferred to the main city it also typically does not have wonders, possibly with the exception of golden abyss.
Not encouraging pushing therefore is one more reason to get rid of scaling troop size with extensions and wonder levels!