I remember it taking 40-50 hours to play through. It's very good though, and I'm happy to stick with it :-) There's about 20 missions.

I greatly enjoyed playing Hostile Waters when I first got it from GOG.com. I usually like action-strategy-hybrids a lot, but there's just so few of them. Mainly I love being able to strategically command several units while still being able to directly control any of them. So, Hostile Waters came as some sort of a godsend for me, even though I was a little late with playing it :)
Unfortunately, I found the mission structure to be too monotonous, as most missions work very similarly to typical real-time strategy games. Defend your position, collect resources, fortify some more and then push onwards until you destroyed the enemy base. I also disliked how the game relied just too much on your direct control of the units. I was actually glad how well my teammates could hold their own, but when I was attacking they just couldn't keep up and rather got destroyed quickly if I didn't watch out for them a lot.
Still, all that didn't prevent me from playing through Hostile Waters, what did it was one of the last missions that I am stuck at, the one with the dissassembler cannon. It basically combines the things I disliked most about the previous missions. A pressing time limit, overwhelming enemy forces and tediously taking out lots of turrets one after another on your own. Lastly, after several tries, reading a walkthrough a still failing I decided to spare myself the frustration and rather give up.
As bad as that sounds, I definitely won't forget the good time I had with Hostile Waters despite its shortcomings and that it really is more than just a nice prototype of a rather unique genre, but a very coherent and fun game in it's own right. It's just too bad that I will also likely never finish it :)

I'm enjoying it so far.
I know what you mean about having to take out too many turrets.. but other than that i've been enjoying it a lot.
I wish i could get the hang of using the direct orders a little better... they work well, but in the heat of the battle i just always end up going to the battle map and giving orders that way. They should have given the battle map a countdown timer (like Space Hulk).
The AI has been surprisingly good, and I've been reasonably surprised by the number of different approaches i could find to some of the missions. (finished one mission in about 3 minutes using a scout and the cruiser's guns ;-) )
I just wish the missions were a bit shorter... i don't have as much time to devote to games as i did when i was younger, so i really appreciate games with scenarios that can be completed in under 30 minutes. (Darwinia or World of Goo, for example). It makes it much easier to play in small doses and still feel your progressing.
Good story and characters too... recommended.

Anybody here ever get the game to run on cheats?

I loved this game. Played once through, second playthrough is at the final level. I would have loved a skirmish mode, just some thing creating a random map, random size, and random starting positions...