OK, but there is one problem: either we make Europeans able to ship 25 000 armies to America or we restrict their numbers but create Colombian Epidemic mechanic which wipes out 90% of indigenous population (in eu4: -90% of manpower, economy, army decreasing slowly over decades).
A false dichotomy fallacy isn't going to carry your argument very far. I could easily say "either we deny Europeans shipping 25000 soldiers or we allow natives to build early carracks", and then simply claim that the disease is modeled perfectly well with the ridiculous tech cost abstraction instead. It's the same approach. Besides, the only time this is possibly relevant (player using new world nation), these regions are going to be far more unified than history ever dreamed, which makes forcibly abstracting such an advantage to the Europeans even more awkward.
But to me this is an annoyance, not some game breaking alteration.
Honestly, the only things in this patch that I find immediately unsettling are the 'natives can't build boats' thing and the lack of mentioning of fixing rebel defection logic. Aside from those, this patch looks pretty alright.
No, let's not forget about the other awful one. Show me that subject nations finally work (IE they core and convert religion consistently, rather than doing nothing for 30 years or more) alongside rebels being less derpy and I'll still peg this as arguably the best patch to date in spite of the annoyances, unless they're dumping hidden changes on us again