Thanks for the thoughts guys; much appreciated. Regarding the questions that were raised, I'm playing with the Ultimate Edition which has all 3 together, so I assume I'm actually playing the TA game mechanics then (Don't know for sure as this is the first I've played GalCivII). Although, they've clearly disabled espoinage for the campaign (except to assign agents to the whole race) so maybe it's tweaked from TA somewhat. What I meant by only having success in orbit is that up to that point I'd only had success while I was defending my own planet (never attacking), and that was with the orbital command center...
Clearly it would seem that the tie rule is what's causing it. When I attack with him down to 1 HP, obviously with 20+ attack I'll knock it down, but then he gets his shots and naturally my ships all die too. Then he has the stronger ship with his 200 attack, and I die. I imagine with the original "attacker shoots first" rule in the original version that wouldn't have happened; I guess it's just a matter of the new engine not really playing nice with the old scenarios. I was eventually able to win regardless; throwing fleets of 5 small ships at his 1 HP with combined attack of 80 seemed to result in about a 1/4 chance that I'd knock him out. I still think there might be a bug on account of my attacking him with 1 HP and after the battle looking to see he's back up to 14 or so.
As it turned out, in the next Apocalypse scenario I gained even more familiarity with handling them. I'd built up to phasors and had about 120 attack in a fleet of 5 small ships, and it seemed like escorts and scouts could be taken down as you'd expect, but the cruisers had the same issue; about a 1 in 4 success rate. I think there's more to the tougher ship calculation though, than just attack power. What I found was that if I built a medium hull loaded with extra HP, even taking a single ship in with 16 attack, if he was down to 1 HP my medium ship would survive with 5-15 HP left out of 50 or so... Considering his attack is something like 180, I'm suprised he wasn't taking out my 50 HP in one shot; maybe he was but I was getting the benefit of the tie rule... Who knows... It would be nice to know the exact mechanics at work though...