Frankly, I like the idea of slowing down rebel fleet by destroying cruisers/battleships very much. They're quite hard to encounter in fleet-occupied sectors (amongst corvettes, destroyers, etc.), and even more rare in normal beacon's special events. It seems logical, that blowing their mainbone assets should slow them down. I wouldn't have anything against making them harder to kill, though - by increasing their hull toughtness *and* crew-members count considerably (and/or one or two special, separate weapon system - in addition to normal one - like on Vindicator federation cruiser, or rebel flagship?).
Also, please, don't take let's play suggestions as granted for feature implementaton/removal. They (let's plays, not features

) tend to be quite situation-dependant, rarely well-thought (while doing such video, you're thinking about 156456 other things, than how merit is your actual idea/rant). For example, from my experience, delay from destroying cruisers have some randomization in it (just like delay from hiring mercs have) - which may explain why some thought it didn't slow rebels at all, if they were unlucky - but, I haven't made any scientific tests on it, so...
/Estel
// Edit
Inspired by re-use of assets question - it might be worth to clarify this mod's license. If you would apply CC (Creative Commons) to you work on cruiser= new drones apperance, etc., and GPL to code, people would know that they can re-use your work for their mods (and how - i.e. not for making money of it, without your permit). It is perfectly legal to apply GPL/CC license to mod content, even though FTL itself is propertiary.