From what I can see there isn't anything fundamentally wrong with Jr., it's just that parts of his kit were undertuned in 4. None of the changes mentioned reference damage changes, which shouldn't be difficult to compare since all the matches have been items on.
First of all, nice profile pic!
From what we have seen so far, there are so many things that are just fundamentally wrong with the Ultimate version of Jr.:
1. I'm not sure if it was changed, but in the E3 demo, you couldn't run through the opponents shield. This also applied to Foxes side B. I haven't personally seen it, but I would assume that Bowser Jr. can no longer go through the opponents shield with side B, which is a pretty significant nerf.
2. Mechakoopa (MK) is horribly unbalanced from what we have seen. Firstly, MK no longer bounces, which isn't too bad, but it will make some setups harder to pull off. But then we start looking at the bad changes. MK now just drops in front of the opponent when they shield it. It no longer goes through shield. Now all the opponent needs to do is shield and they can very easily pick up the MK. Another huge nerf to the MK is that picking it up twice no longer gives you immunity to its blast. This nerf just discourages creative setups.
3. Hitboxes for almost every move have been reduced. Up tilt, Side tilt, Down tilt, Up smash, Up B hammer swing, and grabs have noticeably less range. Up B hammer swing was already difficult to land consistently, so this just hurts.
4. Forward Smash now has more ending lag. This change makes no sense. In patch 1.1.4 of Smash Wii U, Sakurai changed this move to have less end lag, so now he is adding the end lag back? This was the only semi-safe kill option we had in smash 4 because if the low end lag, so now we really don't have much.
5. Throws don't string into anything, although they didn't really lead to any combos in smash 4 so this doesn't affect us too much. The most you could get is down throw dash attack at very low percents and that's only if your opponent was brain dead.
Let's look at the very few positives though:
1. Jumping out of side B no longer eats all of your jumps. You can now side b, jump out of it, and double jump. If you were good at managing jumps in smash 4, then this really doesn't matter all too much.
2. Jab is more reliable, and kills at 130% on ledge. But killing at 130% at ledge isn't that great if you think about it. This means you have to punish people on ledge with jab and they have to be already at a pretty high percent just to get a kill. Back throw kills at ledge at 160%. Again, this isn't that good compared to other characters kill options.
3. There is an ending lag buff that every character got.
I really want to continue on with this character. He has so many movement options and he is always super fun to play, regardless of win or loss. We can only hope that the first balance patch in February helps us out.
I know there aren't many Jr. mains out there, but for the few who check this thread, would you guys want to make a discord server for the Jr. mains? We could share new techs and combos to try to make this character more viable than he was in smash 4.