While I don't go trying to take down small rubbish fleets, even carrier groups run.....
(Also, if the Atlas is slowing you down too much, that's probably because it's hugely overkill for the purpose. Either add a couple of tugs/Unstable Injector/Navigation level 5, or ditch it and get some destroyer-sized freighters or Hounds. Or just don't use freighters at all and accept the couple of days of 0% LR for hauling the loot to nearby stations, although this has complications of its own.)
If you're taking on planetary defense fleets or large supply fleets, the Atlas is absoloutly necessary. In fact I often have 2 of them to be able to transport all the loot, I then need 4 tugs + 10 nav to remain competitive in terms of burn speed. Using these guys I can reap about 500,000 to 1,000,000 credits per hour.
Anyway if the game is to be more 'interesting', I'd look at implementing Fleet formations
http://fractalsoftworks.com/forum/index.php?topic=6847.0 which affects more on the combat gameplay, not to mention the many suggestions of radar and electronic warfare are numerous in previous threads including one of my own.
The implementation of some sort of 'stamina' constraint is necessary for any game, but the current implementation doesn't really make for decisions that are genuinely interesting. It has only slowed me down a bit, and forced me to change my fleet composition to ships that aren't as CR dependant. I'm not saying I 'hate' CR, I just disagree with it's current implementation regardless of future addition of industry.
After looking through the ship_data.csv the one conclusion I can come to is that CR is direct penalty for ships that are more effective in combat. It's like CR is a means to constrain ships that are 'better' to make them on par with 'cheap and lesser ships'. So although there are different tiers of ships, the ship tiers are made meaningless by CR. It's kind of like 'you can use a hammer all day for a few nickels, or you can use a nailgun for $50 for an hour...before it overheats and you need to put it in the corner...and then pick up your hammer anyway to just finish the job.
Looking throughout the CSV and codex, technology becomes an excuse to increase CR. It seems as if the intention is to make all hulls in some way 'equal' so that someone with a large 'cheap and cheerful' fleet can take on a 'expensive and effective' fleet. The expensive fleet may win round 1, but the cheaper fleet then wins round 2,3,4 etc. because it has the stamina to finish the fight.
This then prompts the question if players want ship tiers that actually means a 'better' ship really is 'better' in every way as ATM CR also levels the playing field.