Hookay, after toying around some with the selection based empire tree...
In a few words: I find it better/more useful/easier than the default.
In more words:
The thing I didn't like most about the default empire tree is that *everything* was in it and on larger maps it was always easier to just say screw it and find what you needed in the main view than bother with the tree. The only time I really used it was in combat to pick targets, or when I needed to pick out some select ships from my fleet. I never used it to do planetary selection/production/what have you, it was just slow that way.
Selection based empire tree is a lot easier to navigate, mostly because it only has things you want in it and not a ton of crap you don't care about

Now you don't have to scroll through every planet listed to find one you need, you can just create a control group with the few planets you need. Clicking on a planet automatically expands the tree for it and shows you all the structures/ships which makes it very handy for people who don't have time or don't want to zoom in on a battle, it's easy to control after just one click.
All in all, as I've mentioned, I think the selection based tree is a lot less cluttery than the default and makes it easier to get to the things you need quickly, which is a big plus.
For some other comments, I noticed that if you click on a star, it'll expand all the planets but it won't give you a way to shrink it again without de-selecting the star. It's not really a big deal. Unfortunately I forgot to try it with a star in a control group, but I assume you can shrink those normally, star or not, so that sort of solves that.
The other thing is that to get things up on that tree permanently you do need to put them in a control group. Normally this is fine since you can put the necessary planets into one group and it won't be much worse than having each one individually. But with only a limited number of control groups to share between planets and fleets, on large maps you could run out of groups to assign. For example, for each fleet I have two groups, my main assault force and a second group with Krosovs/colony ships to jump in after the defenses are down or softened enough. On a medium-large map I can control 3 fleets fairly easily, that brings me to 6 groups leaving only 4 (at least I don't think it's possible to have more than 10, foot in mouth if it is) for other things. That's still doable since I don't often have 4 'main' planets I need to keep track of, but on large maps with multiple solar systems you could easily run out of room and the tree would start getting cluttered again because you might have to start stuffing quite a few planets into one group, not to mention run more fleets. And then there's hotkeying enemy planets you want to keep eyes on, etc..
I also remember someone posted that they actually have several groups within a fleet to split it when necessary or combine into one. That all takes up precious numbers

If there was a way to get planets up on tree without needing a control group for it (but groups could still be used if you want several planets and the ability to shrink that branch of the tree), I think that would be pretty beneficial overall. The easiest way I can think of doing this is something like ctrl+click on planet throws it onto the tree permanently, while ctrl+clicking a planet/star while it's on the tree would remove it. Pretty simple but effective, without needing to worry about control groups. The added bonus of that is that the planet icon itself will show up on the tree, as right now you just get the group number icon and have to expand it to see the 'contents'.
Hopefully I've made some sense, it's getting late. But that's really the only suggestion to it that I can think of. Everything else is pretty intuitive and does exactly what it needs to