Storylines...
...well, my favorite would be the one from the last old BGS movie. BSG finally finds Earth... back in the movie it was 20th centuiry earth, and they had to decide to lead their fleet elsewhere, cause that earth would be easy prey for the cylons.
But what if the new BSG finally finds the thirteenth colony, and it is 23th century B5 earth? The BSG would find some serious sanctuary here, and the cylons an opponent to be reckoned with... with powerful allies through the Interstellar Alliance, but the Cylons also might be approached by the Drakh...
Lots of possibilities!
Tech-wise BSG has some strange blind spots, true... but alltogether it can be made to mesh. The nukes are the biggest thing - but then, noone ever said how big a nuke the Bucket took with minor damage; if it was small enough it wouldn't be more boom then an narn e-mine.
An Omega vs the Galactica should be an even match - the Omega is bigger, has better weapons (and a longer range), better defences.
Longer weapon range, yes. And is probably a little bit tougher.
The Galactica has nukes, better all-round firepower, x2 to x3 the number of fighters (and she can launch them quicker), tougher (maybe), EW Raptors to support the Vipers and a pin-point accuracy with her FTL.
Nukes are quite likely not as powerful as the nukes we know in B5 (otherwise it gets unplayable - and please ignore ItB kilotons), so the ship has less toughness too. Less firepower, but more fighters.
Basically I think if the Omega catches the Galactica, it will tear the Battlestar apart. However before that happens, the BS may be able to make a quick jump away, and send it's many, many fighters back to wreck the Omega without ever entering its weapons range. However before they arrive the Omega can jump to a new location and continue the search for the Galactica. Rinse and repeat.
So the outcome would depend on the captains success in playing hide and seek. Whoever catches his opponent first in the disadvantagous way, wins.
In a slugfest the Omega would probably win, though just barely - it might just as likely end as draw, with both ships destroyed.
Of course, that's talking about the Galactica... the Pegasus would be a different Beast entirely... but I suppose that's why the EA built the Warlock!
Starfury vs Viper - good question! I think the Viper is faster but the Starfury has the edge on manoeuvreability and firepower.
That'd be how I see it too.
BSG tech is a bit uneven - for instance they have anti-grav technology and a very efficient jump system; on the other hand their scanners cannot detect lifesigns, their ships and fighters make use of conventional munitions (cannon shells of varying sizes), they have limited defences (no shields or interceptors), nor have they mastered energy weapon tech. Dr. Fanklin seems to have the edge in medical field as well.
All true - the jump system is the biggest anomaly (that good and THAT small - unbelievable. But maybe it's "precursor tech", meaning they fould it among the remains of a long-gone high-tech race...). The AG is no biggie - after 2261 the EA has it too, thanks to IA membership.
B5 tech has the advantage in energy weapons, true - but that's not that much of one, as projectile weapons are not that bad, if a bit short-ranged and less accurate compared to near-lightspeed beams and bolts.
And BSG has nothing, nothing at all comparable to B5 organic tech - except the Cylons "infiltrators" and their "counciousness transfer"
BSG may have interceptors of some kind, at least some crude version - I do remember the tried to shoot down the nukes (but only Starbuck succeded from her Viper). But B5 has dedicated interceptors, something BSG hasn't come up with so far. Shields are rare in the B5 universe, and unknown in BSG... and the advances in med tech may be through contact with alien cultures and knowledge transfer.
Alltogether I'd consider them about equal...
BtW, if someone made such a crossover... another possibility would be "borrowing" from Terminator for the Cylons.
And while we're talking crossovers... I always let a bit of "Aliens" and "Predator" bleed into my campaigns - in my B5 universe, the Yautja exist and occasionally visit on hunting trips, while xenomorphs were created by the Shadows to "spice up the Anthills"...