The fact is do a full boss run is time consuming. Doing it after the revamp, will be even more time consuming, since Bosses will be harder.
The main point I would suggest to change, to not make the whole end game experience a full frustating stall battle, it's remove the bag ban from hard mode. It will totally be not funny with the bag ban. Even more after we get hitted by bosses perma crit or burn or whatever. It's not pvp, it's pve. Think about that, having the bag allowed will solve part of the problem of people considering it too hard.
Second main problem, is the fact that bosses are too far each other. It's very boring to reach them
What I suggest?
To make a huge change to that too.
How?
First of all, divide all bosses in 3 categories: Gym leader bosses (Misty, Surge, etc), Special Bosses (like PC Boss, Terminator), Staff Boss (Neroli, etc).
For the first category, gym bosses, what I suggest is to use the same Koichi system.
When you first find Koichi, inside Saffron dojho, he has a white name, as a regular npc. After you beat him, he turns Red, as a Boss. Do the same for Gym Bosses. When you defeat a Gym Leader in story, he/she turns Red and became the boss.
Special Bosses: you can find an use to an unused tower, this would require some works from mappers, but not too much. Where?
Example: The Battle Tower in Johto!
You make mappers build a base floor with a PC (with Joy) and a mart (like E4) and then a couple of floor with some dedicated room, and the special bosses inside them.
Staff Bosses: the same as before, but in another unused place: Tower in Trainers Valley.
I would say this would require Trainers valley to became a little cheaper for people who don't have trains pass.
Think about this please. It would remove two of the most problematic thing about bosses and the revamp.
Thanks.