1. Combine multiple bonuses into individual nodes and reduce the overall number of nodes.
For example, the firepower tree might have "Accuracy Boost" which provides both a projectile speed bonus and a laser duration reduction. Combining firepower nodes like this would allow players to switch their mech loadouts without redoing their skills, and it wouldn't favor boating.
In other skill trees, nodes could contain a combination of a more useful bonus and a less useful bonus, so that players can progress without being punished for it. For example, "Skeletal Density" might provide a leg damage reduction in addition to the structure bonus, while "Armor Hardening" might also provide a crit chance reduction.
2. Combine the skill trees to create an "offensive tree," a "defensive tree," and an "equipment tree."
Currently, the large number of trees adds to the confusion a bit with some trees seemingly more essential than others.
The "offensive tree" could contain the firepower tree plus the heat containment and cool run skills.
The "defensive tree" could contain nodes from the survival tree along with nodes from the mobility tree.
The "equipment tree" could contain a combination of nodes from the jump jets, operations, sensors, and auxiliary trees.
These last four nodes are, in my opinion, not nearly as essential as offensive skills and defensive skills, so the "equipment tree" nodes should provide a larger set of bonuses to make the point expenditures more worthwhile.
3. Allow a limited number of points to be spent in each tree plus an additional number of points to be spent in any tree.
Right now, there are some skills that are essential and others that are optional. Generally, by the time I've spent my points on all of the essential skills, I don't have enough points left over to try out much else. I'd prefer it if I could spend a handful of points in each tree, while still investing most of my points into specific areas.
For example, if we had half the number of nodes and only three skill trees (as in my previous suggestions), we'd only need half as many skill points. From here, I'm suggesting that we have a 10 point limit on each of the three trees, but allow an extra 20 points to be spent wherever we'd like (for a total of 50 available points). This way, a player can get some basic bonuses from each tree while still specializing in one or two areas.
I realize that there are already lots of ideas out there and I'm not claiming that these suggestions are THE solution. I'm just hoping that these suggestions might have some useful elements.