First off, my standard disclaimer…
even the worst BSG is BETTER than what currently passes for TV these days…
that said, i have noticed the eps getting a little weaker and more “Star Trekky” and i don’t like the way that it’s going, they need to stop frakking around with a proven formula, that said, here are the changes i’d make;
Ron Moore, you are no longer permitted to do “Flashback” based episodes, with the past 3 or 4 eps, you’ve beaten that plot device horse into a fine red paste, if i may mix metaphors here, you’ve used up your “flashback ep” allotment for this season, all the remaining eps must have a conventional timeline…
to nip it in the bud… NO TIME TRAVEL EPS, EVER!
you’ve also used up your “self-contained eps” allotment as well, if you’re going to introduce a major villan, whether it be a human, a Meatbag Toaster, or a Raider, give that character a decent story arc so we can learn to hate them and rejoyce when Starbuck, Apollo or Kat greases them
NO TECHNOBABBLE ALLOWED
Drop the “Magic Pop-Tart Blood” (or rather “Magic Pop-Tart Filling” 
) plotline, it smacks too heavily of BAD TNG Trek, thankfully you’ve only used this plot device once, let it slide
and on that note, since i’m not a fan of kids/babies (especially not magic/Übertalented kids/babies) or kids/babies in sci-fi shows, drop the “Pop-Tart” thread entirely, adding a baby to a sci-fi show is a bad idea, especially a “magic baby that can change everything”, maybe have the Pop-Tart have a Kernel Panic or something, or have the Toasters abduct it after it’s born (therefore giving Boomer a reason to completely turn her back on her Toaster side and perhaps be re-integrated into Galactica’s crew)
i know the Mark VII Vipers are more sophisticated and better armed (3 cannons, the two on the main wings, one on the rudder), but they just don’t have the “feel” of the classic Mark II’s, don’t completely eliminate the use of the MK II’s, the VII’s just don’t have that “Real Viper” feel to them anyway
admittedly, Toaster battle strategies have changed, now that when they die in a dream, they’re dead for rea…oops, sorry, thinking about “A Nightmare On Elm Street” there… err…when they die, they’re dead for good, still, the Rag Tag Fleet is hurting for resources, especially metals for constructing Vipers, why not scavenge the metal from the Raiders you shoot down…
and on that note, why not have Balty get HeadSix (or even Gina/PegaSix) to help design an EMP/Virus weapon to use against the raiders, something to shut down their organics and allow the disabled ships to be captured, lobotomized, retrofitted with Colonial flight controls and instrumentation, and used against the Toasters (or do a Terminator 2 on them and reprogram them to attack the other Raiders and/or BaseStars), maybe Balty’s assistance isn’t even neccecary, have him design the EMP/Virus weapon
Rebuild the Blackbird, and make more of them, a Stealth ship is a valuable tactical resource
what would you change to improve/shark-proof BSG?
