With regard to individual city growth: don't big cities generate equivalent big bonuses in Civ 5? Isn't that how you win a culture victory, or hang in there in a Tradition science game?
My one-game-removed opinions aside, do you see any way to generate equivalent effects in VP?
To your last question....no, to me it would take a major rewrite....and ultimately would be a different game. VP has made the best version of Civ 5, but rewritting the core economic tenets would make it something else. At the beginning of the project maybe it could have been explored...but as Gazebo said the major parts of the project are done, and I agree with that. Its time to tune and tweak but the time for big rewrites I think is done. Its time to move on.
To your question on Tall Cities, hehe its not even close! Percentage Bonuses were much more frequent in Civ 4 compared to Civ 5, and VP has made it even less. In VP, the majority of bonuses are flat, static bonus...and many of them are generated from specialists as opposed to worker yields. Now...that model has its own advantages, one of the things Gazebo has cited is a smoother scaling into the late ages, and I think that's a valid argument to be made. However, the consequence is that cities become more equivalent.
Imagine two cities: A and B. A gets a 50% bonus to gold, B gets 0%. If you could add a new building that gave +4 gold....where would you want to put it? City A of course, you get more value. Take that one step further, if you choose where to put your workers, would you want to grow a pop in A and work a gold mine, or do it in B? Again, the answer is A. Further, the stronger the percentage difference, the more you would tend to choose A over B.
In Civ 4, percentage bonuses were common, so with planning you could make a capital city that carried a 100% magnifier to science compared to another city (honestly I'm likely underestimating it here, but my memory is not strong enough to go higher). So growing that capital was a big deal! And therefore, happiness was a big deal. In Civ 5 VP, you are talking 10% magnifiers, maybe 20% at best in the capital until very late game. Therefore, centralizing in your capital is not as big a deal. Honestly....the biggest multiplier was actually in tourism with the National Visitor Center, which basically doubled the bonus of tourism in your capital. That's was one of the reasons why I argued so strongly for it to be changed, as it went so starkly against the flat model that everywhere else in VP had been pushed.
One more point, since you mentioned culture victory and tradition science victory. Its not that Civ 5 gets "big bonuses" for Tall cities in the same way that Civ 4 did...its there is no bonus for more cities towards these victory types. For example, culture takes a big penalty in Civ 5 when you get more cities...past a certain point you gain policies slower than a small civ does.
When considering tourism, tourism is primarily generated through:
1) Specific GP (Artists, Musicians, Writers) which are primarily generated through guilds only buildable 3 times. So large or small...your empire can only generate these so quickly.
2) Trade Routes: Again big or small, you can only have a max number of trade routes.
3) Archaeologist Great Works: You could argue this is an advantage for wide as they have a hammer advantage to build more archeologists. There is truth to that, but its a short window, and I found tall civs that dedicate to archaelogists briefly can still do just fine. Honestly this is more of a science fight (getting to it first) than a hammer one.
4) Late game culture generation and great works through the hotel, airport, national visitor center, and stadium if I recall. These tend to reward focusing of culture buildings and centralization of great works (especially with the National Visitor Center....though much less now with the recent patch), which again favors "Tall".
5) Chanceries: This is new X factor. Now that chanceries can generate tourism, that gives Wide a bit more to work with.
6) The tourism multipliers: The most important one here is the "I have a smaller civ than you do". There is a built in advantage for smaller civs going culture victory baked right in, and its not a trivial bonus at all.
7) Aesthetics Tree: Some really strong tourism bonuses here, and small civs that gain policies quicker can get through this tree faster.
So small civs have the same tourism benefits as large civs....and even have a few key advantages. This is why small civs often go culture victory.
For science, the same thing occurs. Because of the permanent science penalty for new cities, new cities stop generating net science bonuses, and actually are often science drains. People have argued that this balanced by the fact that more cities can generate more great scientists...whose yields are based on total science output. I think it helps, but in my experience small civs are better at science than large ones. However I don't think the difference is as great as tourism is for small civs, so I think science is reasonably balanced with a tilt towards small (which is fine, I think its fine for small civs to have an edge here). Large civs have bonuses in hammers and gold, which is why they excel at diplomatic and military victories, which is perfectly fine.