I tested the new update this weekend, and I have to say that even if I was handed my own ass in my first attempt, I'm liking the CR mechanic.
Before, all I would do was to slowly creep to a small high tech fleet, and then proceed to steam roll anything that crossed my path, starting with the pirates, then independents, the TT and finally the Hegemony system fleet. Every single playthrough was basically the same, just change the ships and factions if I was playing a mod.
With the update I'm still manning a wolf frigate (starting ship), but I still got myself a small high tech fleet (in order I got a medusa, a gemini, a wing of daggers and xiphos, then a second wolf and finally a paragon). Since the first playthrough I've got no problems with supplies, or ship speed issues (a max burn of 5 is more than enough to chase other supply fleets), but more importantly I'm using a different ship composition and usually changing which ship I'm controlling to mantain CR an not just deploying my strongest ships in every battle.
The only negative aspect of the update is the harry mechanic, which is just broken, and unfun; I mean it's just easy mode, since you can easily drag the enemy CR to 0 and then just kill the larger slow supply ships and get their loot with frigates.
I guess making ships able to fight at CR 0 could help with that, even if it meant being severely handicaped (dunno, maybe halving several stats, like flux regen, shield strenght, fire rate, etc), and it might also help in situations where the opposite is true and you're left with only 1 ship and no way to regen CR, avoiding the deathspiral that other players have mentioned.
However I would be more happy by adding some restrictions to harry. I thought maybe adding a temporal decrease to the maximun burn, something like if you chose to harry, the enemy gets its CR reduced but you get your max burn reduced by 1 for a day, if you can still catch the fleeing fleet and chose to harry again, the enmy CR gets reduced again and you get the harry penalties added on top of what you had, so max burn gets reduced by 2 on a 2 day coldown. This way you can only harry the enemy fleet as long as your fleet can catch it. I originally thought to just reset the timer, however that way you could just easily wait the time and then catch it and repeat.