What brake pads are you using? Same as those you were using before? Also, how much did you adjust your brakes when installing the wheels? You may need to just increase the brake width. If the brakes are engaging as soon as you start squeezing the lever, you may not be applying as much force as you could be if your brake engages later along the lever stroke, if that makes sense. Assuming your wheels fit inside the brake pads, brake width compatibility is probably not your issue.

Sounds like the might be similar brakes to what I had on my old propel, and if that's the case than they might just be bad brakes. Did they work fine with the stock wheels?

Thanks for the quick reply

I'm using the swiss pro carbon pads (the yellow ones). These were the same as my previous bike however the brake calliper had more space clearance than on that one. Here I've adjusted the callipers to the widest possible option yet the space is very limited.
Just to fit the wheel alone, I need to deflate the tyre to make it go through the calliper (and it's quite difficult). The difficulty to adjust it afterwards probably impacts the braking efficiency given its somewhat asymmetrical as a result (more for the rear wheel though)

I did a bike fit a few months ago and the bike fitter who was somewhat specialized in Bianchi bikes seemed to be of the view that the mavic wheels could be too large but I didn't dig further at the time. The stocks wheels have an aluminum rim and they were narrower so it's not directly compatible

Your reply just made me think about "narrower" brake pads - which I haven't looked into if that exist; maybe a much simpler solution?

I suspect the lever pull is your issue. There also are probably small screws on the bottom of each side of the brake caliper which adjust spring tension and will let you center them.

I'm not aware of narrower brake pads, but it's not uncommon for people to file down their brake pads to make things fit better. Not exactly efficient, but unfortunately probably not a better option