No, it is a crutch like Surveying and Salvaging, if you do not want the skills. (Well, I want them to be on par with officers, but not by giving up everything else as per OP.) If you take the Industry exploration skills, you get the money and some rare stuff and have no need for bounties for a while.
But demanding everyone take pilot-only skills immediately just to have a chance to beat bounties that upgrade faster than you can expects too much, just like expecting everyone to sink nine points into Industry (for Surveying and Salvaging) to get enough money if they are not proficient enough in combat. Exploration is fun, if it did not gimp combat power.
Bounties were not broken without level scaling. With level scaling, bounties upgrade too fast, at least it did when progression was 4x. (I suspect they still level up too fast at 3x+10.)
But 0.9 has toned down level scaling so that problem should not last for much longer.
But punching a class or two above your weight solves literally every problem you say the game's combat has.
Not every enemy that is not a pirate will be unskilled. They will have the skill advantage over you unless you pump all points into combat stuff. Yes, player can exploit AI vulnerabilities to beat the AI with an unfair advantage, but it still does not feel good.
Also, if I put everything into personal combat, punching a class or two over unskilled enemy is not enough. I expect things like frigates soloing an entire pirate fleet or an unskilled battleship, or a battleship soloing multiple fleets without much difficulty as done before 0.8. Even Tempest could solo the Hegemony Defense Fleet during 0.6x days, but it was not easy.
The pursuit of optimization has made the game harder, which begs the question of what exactly you are optimizing for.
Simple. Maximum power at the end, even if early-game is extremely brutal and unfair.
To clarify: "pursuit of optimization" might make it harder in the beginning and short-term, but if you survive to the end, you are even stronger than if you did not take the power option.