Picking something unconventional and just running with it isn't really a style. If there's a real benefit to that unconventional method over what's commonly used then it's worth trying, but you can't fly your ship backwards all the time and expect victory. You have to keep in mind your crew probably wants to win as well, it's a bit disrespectful to deny them that for the sake of novelty.
Whether or not you deserve that flak you speak of is simply a matter of results. Win with it, and you're justified. Lose with it, and you deserve your crew's ire. If you're not confident about your unorthodox playstyle, at least check to see if your team is fine with experimenting with it.
That said, I can see some situations where an engineer would be more useful than a pilot, such as on a sniping galleon. There's little need to move and it's best if all three guns are blaring. The same can be said for a Spire, that takes pressure off of your top engineer. What I find myself doing, however, is just gun in my engineer's place. I'll take charged rounds and just take over the gun while my engineer continues repairs. You're almost always going to have at least one engineer on board, and if you can simply take his place at a gun you don't have to sacrifice the much more generally useful pilot tools.