Right, well I have my b agile and carrycot combo... initial impressions are positive for what I wanted it for (nice wheels, lightweight, fairly easy fold, takes full size carrycot, under £250) but I definitely think it's not as easy to use as a baby jogger. In fact for your purposes, where you will most likely be wanting to lift the carrycot off on a very regular basis then I think it possibly wouldn't be that great as it is an extremely tight fit with the seat fabric on.
I have removed the fabric but you need a screwdriver and some patience, doing this is not in the instructions so I'm pretty sure it's intended to be used with the seat fabric still on. Also the basket comes off with the fabrics at the front, you'd have to find a way of re attaching it to the bare frame. On the plus side the cot is easier to put on and off in this format and it looks better IMO.
The seat fabric removal on the city mini is both easier and something it is specifically designed to do if you want the carrycot on the frame only. Equally you can use the carrycots with the seat fabrics on and from what I saw in the shop the cots are easy to take on and off. The baby jogger compact carrycot does what it says on the tin though, it is definitely compact and doesn't have a carry handle.
If you wanted to go in the bagile/city mini/pull to fold type of direction and are willing to pay the extra then I think on balance a city mini 3 or probably 4 is a better bet when compared directly to the b agile. Possibly with a deluxe hard carrycot instead of the compact one?? Just my opinion, my ideal was probably a city mini 4 with deluxe carrycot but with raincovers, bumper bar, cot etc. the whole lot was stacking up to approaching £400 and I'm too much of a cheapskate!
Good Luck with your choice 