Of course as any other new system, the Skill Tree requires some amount of a small tweaks and polishing - it's not a problem at least for me. But there is a very serious problem - only one problem, which able to ruin the whole concept of the new system. As I can see, the Skill Tree is supposed to encourage variability of the mech builds, but the current build of the system does exact the opposite.
I found that there are only TWO (!) main (meta) variants of the nodes sets, depends on a type of installed weapons (ballistics or energy). I assure you, that there aren't any more variants if the players really want to master (maximize) their mechs. You just can't exchange the speed tweak for the arms angle, or the radar deprivation for the UAV improvement, etc. As well as you can't exchange the "must have" nodes mentioned above for a secondary weapon type branch. They aren't equal, the second isn't worth the first, and will never be. Also the JJs and the Aux branches will be abandoned forever, while there are much better branches and you have limited SP shared between all of the branches.
Furthermore while you can (must) have only one weapon type skill branch (if you want to be max-effective) and mastering mechs became longer in the new system, you will never want to invest your XP points (time) into anything else except the tier one top-mechs, which are much more suitable for monotype weapons boating due to their hardpoints. All other mechs will become underdogs as never before. It also ruins previously perfect synergy in the sets of LPL+ML, SRM+S(P)L, Gauss+PPC, Gauss/UAC+Lasers, etc.
So what we have as a result:
1. Monotype weapon boats based on the top-mechs (like quad-UACs, or pulse laser-vomits, or pure SRMs, etc. on Timbers, Marauders, etc.);
2. The player has only two ways to maximize his mech, and the way depends not on his will, but only on the type of installed weapons.
I don't think, that you wanted to make the new system like that, don't you, devs?
Here is my suggestion how to deal with it.
Maybe this isn't so obvious, but the root of the problem hides in combined together offensive and utility skills - shared SP points between them. Thereby there is a need of reworking a base principle of the new system: separate SP points into offensive SP (OSP) and utility SP (USP). OSP should be enough for a two weapon branches or a one weapon branch and an auxiliary branch (MGs, Flamers, NARC, TAG, UAV, Artillery, Air Strike - for support builds). USP should be in current amount minus 20 SP previously spent on one weapon branch and maybe plus spare 5-15 SP for the variability (for JJs or torso nodes). And that's all - the simple and effective countermeasure against boating that returns a lot of variability as before. Maybe adding restrictions to add variability sounds weird, but it will work. Also it looks like easy to implement.
And I have one more suggestion for the future improvement of the Skill Tree system. I understand, that this one is much harder to implement, requires hard work, and will take some time, if you will like it, so it's just a thoughts about the future (isn't something I expect in this month or even in this year). My suggestion is to evolve the Skill Tree into the Engineering Department (sort of). The key concept of it is upgrading each specific gun just like each specific mech that will get rid of the half-measure of the separating SP points. In addition it will add to the game even more variability and fine-tuning of each specific build. From the frontend it will look like compilation of a technical project for the engineers (in the Skill Tree interface) and submitting it with all mechs and guns to the engineers' job queue (kind of a factory). It will take some time, during which you won't be able to use submitted for upgrades mechs and guns. Also it's a fair way to reap from impatient players some MCs for prioritizing their project in the queue and completing them right now. As well such system has a lot of common sense, something like: "Hey guys! I'm respected pilot; I bet you heard about me. How about upgrading my mech and its guns?" - "Hey man! Nice to see you! Sure thing, what do you want exactly?" - "This, this, this, and this... and... maybe this... yes, this." - "Ok! We've just added your project in the queue. But... if you don't wanna wait... you know... some MCs could help us find a reserved spot for you at the beginning of the queue." This simply adds the feeling of the real upgrading process (not just one click to upgrade that feels so synthetic and unrealistic). Balance issues can be fixed by changing tonnage and size (slots) of the upgraded gun. Also there may be upgrades for decreasing size/weight, which also decrease firepower/range a bit and can't be combined with upgrades for increasing firepower/range. And… I have to stop my thoughts right here, 'cause there are too much to discuss, but this post isn't about it.
Side notes (for devs if they're reading this):
I hope that my suggestions will be useful, and you didn't too much tire while reading the long post. Also sorry for the grammar if I mistook somewhere (English isn't my native language).