I have been on long protocol for both of my cycles, and my friend has been on the shorter 'flare' protocol. With the long protocol you get pretty much all of your schedule set out right from the offset, with the short protocol you'll have to go for extra scans and blood tests at short notice - my friend ended up booking a whole month's leave from work as she didn't know when she would be needed until the day or so before.
The clinic we were at felt that she would be better with a short protocol, as her AMH was low which they felt would mean they wouldn't collect that many eggs, and the short protocol literally used what she did herself every month, and then gave it a boost. If your AMH is within normal parameters, you don't need to boost your ovaries, as you should respond well enough to the stimming drugs. The lupron will suppress your own hormone production in the long protocol, whereas with cetrotide, you're not suppressing your own hormone production so you need something to stop you from spontaneously ovulating.
I don't think you have any less medication to take when on a shorter protocol. It's quite weird actually. Me and my friend have our AF around about the same time, so while I started taking my DR drugs on CD21, she had to take a drug to delay her period, to bring her cycle into line with the clinic diary. The 2-3 days after stopping that drug, her AF arrived, and then she went for a scan and blood test before starting stimming. On approx CD5 she had to take cetrotide as well as her stimming drug. We ended up with EC a day apart, except that I knew exactly when mine was going to be from approx 6 weeks ahead ...
Anyway, I'm sure after all that rambling I still haven't answered your question
If it were me, and you have a choice, I'd go for the long protocol. It might seem as though it's going to take longer, and that would depend on how far ahead your clinic's diary is filled, but you don't have as many scans and blood tests to do. And if you're anything like me, you'll do your best to avoid blood tests - injecting my tummy is no problem, but don't stick a needle in my arm....
Good luck with whatever option you go for. If you still confused - which I'm sure you are - ask for the clinic's advice.
xx