Bit late to this...
My Baja is my #1 tele (although my CIJ 62 custom is probably better made).
I have to admit though, I didn't reckon much to the pickups at all. I kept it stock for a good 6 months and just wasn't getting what I wanted out of it. I bit the bullet and went for Blackguard Flat 50s, and I was in love the minute they went in. In comparison to the BG50s, the Baja's original pickups were thin and weedy sounding - that might actually be perfect for other folks, but I was actually thinking of getting rid of the guitar when they were in it.
One thing I did wonder, when I was changing the pickups, I found that there's a treble-bleed capacitor in there - that makes pickups "weedy" in my experience - I ripped it out as I put the BG50s in. So I tried the Baja pups later in a CIJ 52 tele (treble-bleed checked for and removed!!) - and they were just as thin and weedy in that one, less pleasant than the pickups that were in it already. Instead I got another set of BG50s and that guitar was sorted as well - not quite as stunning sounding, for me, as the Baja, but lovely all the same.
I'd highly recommend the Baja - the only thing I changed was the pickups (and, er, the frets :lol:). The bridge stuff works for me, intonation is fine. And seeing as the bridge on a tele contributes so much to the tone (or so I understand), I'm not messing with this one now that it sounds like I want it to!