I have both systems. MT in 6,8,10 and 12mm, and ER25 upto 16mm.
The ER collets are used almost all of the time, unless there is need for a bit of extra headroom.
The advantage of the ER collets is that each collet has a range of 1mm, (in all but the smallest sizes, then 0.5mm ), so can be used to hold Metric or Imperial cutters.
Mine are used to hold work in the Rotary Table, as well as milling cutters
They can also be used in the Lathe for work holding, even if of a slightly non standard size.
So ER would be my advice.
Howard