Ah, well, you've picked probably the two most popular major complaint's, I have to admit I was hoping for something more exotic.
With those (as with most anything in the mod), I'm willing to be convinced on them. The reasoning behind the indy change is very simple: everyone uses the indy scouts/troops leaders to the exclusion of national ones. The national ones could be made 0 gold and they would still not be chosen vs default priced indies, due to fort slots. That said, I have been playing with the idea of instead differentiating national commanders by giving them extra weapons, abilities and stats. This seems a fun idea, but it has a lot hurtles, among which is coming up with enough different boosts, making them all thematic (having magical weapons and HP is particularly tricky), and not undercutting heroes.
The reasoning for the hammer getting harder to get is simply that it's incredibly under priced. People complain about clams... it's not unusual for a hammer to pay off in
one turn. The hammer was already an amazing deal in dom2, now it just so happens to be 25% off in base game. I can understand people being annoyed by the change when they first come across it, but I would argue it actually cuts down mm in addition to improving balance. As far as I can tell, no one really seems to think the base game price is particularly balanced, merely convenient since hammer abuse is so deeply ingrained in dominions players.
In the case of research items, I must admit I am quite astonished at the number of people who use them base game. I don't think I would ever use them other than perhaps the occasional lightless lantern binge. However, it seems lots of people swear by skull mentors and owl quills, so since the change seems to confuse some people I will likely reset it next version. Aside from that, I'm not sure what would be considered extraneous tweaks, apart from simply insufficient ones. There are a lot of items that are rather useless even at the very minimum cost and level, nonetheless I gave them what boosts I could on the slim chance someone might be able to come up with an off-the-wall tactic for them.
Again, I very much appreciate the feedback, if there is one lesson I have learned making CB it's that people are happy with almost any balance or imbalance, but make a change that inconveniences people and all hell breaks loose.