Lets not get into who is the better pilot - integrated or modular. Its the same old song as 509 vs Self Improver and everyone decided that was a pointless argument in about 1997 on this forum.
JAA should break down the barriers a little between the two and the course are now much more similar than in the days of 509. The airline recruiting people will take a good while to forget the ingrained history of you are either experienced, 509 or an hours builder. Its what they know and understand. The new system looks pretty much the same but with different names. It isn't and that fact will take a few years to sink in I am afraid.
It is a fact that a large FTO can help catapult you into a very good jet job and I have seen it happen many many times.
97% of the time this is because the following happens (i.e. NOT because you put OATS/CABAIR/BAE in bold print at the top of your CV!):
Man at BA: I say Nigel, looks like we could take two extra 200hr chaps on the next intake as 2 of our original chaps went belly up and decided to be stock brokers instead.
Other Man at BA: Really? Jolly good, I'll give Bob a ring at Kidlington/Jerez/Cranfield and ask him if he has any spiffing chaps just graduating.
Ring Ring... A hespered CFI's office:
Man at BA: Hello Bob, need two chaps for the March sim courses. Do you have any that got over 85% on their exams and passed their tests first time and are bloody nice chaps?
CFI: Why yes Bob, I know just the fellows, they were buying me beers in the bar last night actually. I'll get you their CV's in the post this afternoon.
Man at BA: Jolly good. See you at the next course graduation bash Bob!
CFI: Excellent Nigel - I promise not to throw you in the pool full of female Swedish foreign language exchange students this time :-)
Man at BA: Jolly good.
Two weeks later the CFI's bright eyed boys are at Cranebank for an interview and a sim course start the week after that...
The above applies to most large jet UK operators particularly those that do some kind of sponsorship.
You don't get that if you train at Little Piddlington in the Marsh.
Compensatory factors may be that at a small flying school/club you may find instructors who are senior Captains in airlines or such people flying about in their Pitts escaping their wives on days off. I regularly used to share a coffee and help pull about an aeroplane being operated by a recently retired Concorde Skipper who held the Transatlantic speed record until quite recently. It took a while to foster him as a contact and it never helped me but it is something that doesn't happen if you are inside prison camp Kidlington/Cranfield/Jerez...
With no airlines sponsoring at present and also not hiring their own cadets in training the large FTO advantage has dissapeared in this respect.
Good luck,
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