At least in the PvP community, it has become pretty much the norm to maximize for either ground or space skills and stick to what you're interested in. I suppose it's actually not that different in PvE. (WHen I was still doing mostly exploration stuff, I avoided ground combat and specced primarly for space. But that might just be me.)
I find this unsatisfying.
One appraoch I can see is to split up ground and space skills into two seperate skill categories. The big challenge here is - how does this change existing characters? Suddenly everyone has to manage two pools instead of 1, and you need a way to force all characters to respec to the new way.
Another approach I could see is approach a "dual spec" solution. You can switch between two specs - maybe specifically only ground or space, maybe just two different ones (so if you want to switch between Assault Cruiser and Fleet Escort builds or two different Kits, you can do that, too.)
If we do that, we need to add new ground skills for all classes, otherwise you end up with way too many skill points and everyone having everything maxed at tier5.
To add the number of ground skills, I would suggest that people could spec also into skills not of their class. THis wouldn't benefit their own kits, but their bridge officer, and maybe also teamed-up player characters. (Say, among all team members, the highest rank for a skill is used and 1/4th is added to your effective skill). This means people can optimize their builds for their choice of BOs (maybe you prefer to be a Science officer healing his Tactical BOs and team-mates)
Add in a "generic" skill tree to cover something all classes (and also racial abiltiies) can use.
For example (work in progress and not really perfected yet) Generic Ground Skills Tier 1 Skills
Fitness (Affects melee damage, hit points, ranged damage and evasion)
Mind (Affects kit abiltiies, shield points, resistance to holds)
Tier 3 Skills
Intelligence (Affects all kit abilities duration)
Willpower (Affects psychic damage resistance and hold resistance)
Charisma (Affects allies/BO movement, hold resistances, and improves the cooldowns of activatable racial traits)
Tier 4 Skills
Athletics (Affects ground speed and hold resistance)
Resilience (Affects natural healing and damage resistance)
Technical Aptitude (Affects shield points and regeneration)
Tier 5 Skills
Scienctific Expertise (Affects all science kit abilities cooldowns)
Engineering Expertise (Affects all engineering kit abilities cooldowns)
Tactical Expertise (affects all tactical abilities kit cooldowns)
Class-specific skills do not affect cooldown or duration, they affect magnitude (e.g. how much damage does it deal, how much resistance, how much healing). We might also want to add some passive effects to some of the skills. (Tactical skills for example inflict extra damage with your weapon, and this would naturally make it a "premium" skill to have since everyone uses weapons, even if they don't use kits.)
BO skills would work like in space - reduce cooldowns.