Here's the GECK stats for the vanilla game basic Big Gun troops and their basic armour for the Enclave and the BoS respectively:
http://img.photobucket.com/albums/v256/suntiger745/StatBoSBigGuns.jpg
http://img.photobucket.com/albums/v256/suntiger745/StatEnclaveBigGuns.jpg
http://img.photobucket.com/albums/v256/suntiger745/StatBoSArmour.jpg
http://img.photobucket.com/albums/v256/suntiger745/StatEnclaveArmour.jpg
As you can see, from a purely game mechanics standpoint, the Enclave is better. They are slightly higher leveled than their BoS counterparts (17 vs 11), they have slightly better stats for their armour (Base AR 49, base health 1275 vs Base AR 48, base health 1075), higher number on the relevant skills (Big Guns, 100 vs 74) and a higher base health (65 vs 50, calculated health 170 vs 125).
Ergo, from a purely game mechanics standpoint the Enclave beats the BoS. The Lore supports this as well (or rather, the other way around).
This was just taken from the Big Gun troops, but a quick check reveals the same thing across the board - the Enclave is slightly better.
EDIT: Just out of curiosity I checked the stats in FOOK2 as well.
http://img.photobucket.com/albums/v256/suntiger745/StatBoSBGFOOK2.jpg
http://img.photobucket.com/albums/v256/suntiger745/StatEnclaveBGFOOK2.jpg
http://img.photobucket.com/albums/v256/suntiger745/StatBoSarmourFOOK2.jpg
http://img.photobucket.com/albums/v256/suntiger745/StatEnclaveArmourFOOK2.jpg
The Enclave is better here as well.
The stats for the NPC's is actually a lot closer. Both have 100 in Big Guns, equal health and points in special (only INT and CHA are switched). The Eclave is lvl 21, the BoS 20.
However, their equipment is where the Enclave's edge comes to play.
The Enclave armour has a total AR of 85 and a total health of 1750, while the BoS comes in at a total AR of 73 and with a total health of 1500.
Ergo, the edge is more noticeably in the Enclave's tech, not their soldiers. Which actually fits the lore better.