Going through my legendaries highlights how stingy this game is. Each page of class legendaries has 1 max aside from Warlock and Mage. I have enough dust for 3 legendaries, and I am being extremely careful with what I want to do. I would need to craft 4 Priest legendaries to even try my Reno Shadowform deck. :-/
The Mad Scientist interaction makes sense once you realize the ordering of the phases and how death processing works in Hearthstone, but it does betray the intent of how secrets are supposed to work so I agree that it should be changed. Secrets are meant to be played around, so they should never trigger immediately once put into play. Same reason why secrets only trigger on the opponent's turn now.
I don't agree with you on how buffs work, however. I don't think there's any compelling reason why a minion's inherent health should take precedence over their buffed health in taking damage. I think it makes sense that buffs are placed "on top" of a minion and so the buffed damage is removed first.
The Mad Scientist ordering is counterintuitive, though. I think everyone is surprised when killing Mad Scientist with Fire Elemental procs the non-existent Mirror Entity for the first time. Also, as I iterated before, I think there should be a limit of 1 secret going off per opponent action. Polymorph going off before Mirror Entity is so annoying.
Re: buffs. I think it's odd that you have a 5/4, and then you Hellfire it - the Hellfire kills the minion giving it +3 health, so now it's just a 5/1. So...what? My big spiral of fire didn't hurt it at all? That's the logic there. You had a minion that was set on fire and took 3 damage, but then it lost its health buff so its wounds are all gone?
On that note, has WotC ever explained the "why" behind how minions heal to full HP at the end of each turn? I've never been a fan of that mechanic - games become so slow in MtG when you both get a fatty and stand off until you top deck a counter.