Kloreep: It is annoying as heck when in a system where you are out-teched and can therefore neither fight or run successfully. It's definitely a disincentive for rolling the dice and going to systems above one's "level" in hopes of scoring it big.
Sticking to systems where the tech is at most a level above me, though, I find it manageable. I should note that I stuck to the Corvette class for much of the game, though, jumping straight to purchasing a Destroyer later on only once I was at double digit millions in credits of worth.
During the first half of the game when I was sticking to trading/mining builds that couldn't always win fights, I always tried to watch my radar while in warp. While warp speeds rarely allow you the time to avoid a group of enemies altogether, turning aside a little adds up to a lot of space due to those speeds, and can mean the difference between coming in smack in the middle of them vs being on their periphery and therefore able to run away using boosters. I also made sublight engines and boosters my top priorities for upgrading, second only to shields.
During the second half of the game after making a merchant's living, I bought that destroyer and started stomping most of the things that pulled me out of warp.
What kinds of ships are you flying? I never tried any of the slower light vessels like the Scarab, Dravius or Vanguard, and I imagine the early game would be a bit different going that kind of heavy-load route.
If this is a way to keep players from taking shortcuts as you mentioned I'd say it's a bad way. Playing well and managing to do difficult and rewarding missions because you play smart should be encouraged and not actively targeted to be hindered. If the developers think this is such a big problem just lower the rewards for those delivery missions instead.
That playthrough I went the Militia route with missions and ships. Only did Mercenary & Merchant Guild missions to get their special equipment.
Hammerhead.
Mastadon.
Tennhausen.
Dravius. Tried it because I thought it looked cool but got stuck with it too long and hated it. The broadsides sucked and it felt like I was looking at a glowing baboon arse most of the time.
Arcturus.
Sorcerer. Only had it the last couple missions and I was a natural disaster. Crashed into everything and just drove right into the thick off it, melt faces and as said crashed into everything there was. Boy that ship is long!
I was at the same Tech level or one above the system I was in most of the time. I like to take my time when playing games like this.
So it wasn't much that I had trouble with the "Engines Impaired" after the first couple times. It's the annoyance that got to me.
1: Hearing "Engines Impaired" followed by "Engines Are No Longer Impaired" constantly for several minutes is rage inducing.
2: If you use a Nul-Grav Booster the only substantial effect it have is that you have to hold a extra button pressed all the time in a fight. An unnecessary annoyance.
3: It keeps you from warping away irritatingly long after a fight ends.
Also the MK4-MK5 leech missile barrage hit me about the same time I got the Arcturus which is slow and that didn't help...
The EMP Ablation helps some but for that price I'd really like to get some more effect out of it.
This playthrough, my second, I'm going the Mercenary road. The faster ships they have helps some I've found. The Sturville mitigates this problem a little bit and I'm curious how the Manticore and Minotaur are going to play regarding this.
I'll probably not use any Dreadnoughts this time. They're just so darn big and slow. Well I might try the Polaris. :)