The Mega ST (not the Mega STe) is the best quality machine of the series. Mechanical cherry keyswitches on the keyboard. Easy access in the case to expand (though the Mega STe/TT had standardized VMEbus and the Mega ST was its own custom thing).
The Mega STe had a funkier case, VMEbus, and upgraded specs, but mushy rubber dome keyboard, more brittle plastics.
I like to collect the Mega as the best of the bunch, personally.
The Mega ST keyboard is indeed the best keyboard of the whole Atari family. My TT keyboard has its rubber dome getting stiff with age. This said, the Mega ST keyboard has one big flaw, its plastic is getting extremely brittle and fragile with age. I had one keyboard drop 1m (3ft) to the floor and it exploded like a glas vase. So if you have a Mega ST keyboard, be very careful to handle it gently.
The expansion slot of Mega-ST is just 2 rows of 32 pins that are 1:1 connected to the CPU pins. Any extension that was supposed to be solderedon the CPU could be put in the slot with a simple adapter (see f.ex. the Volksfarben ISA slot adapter for ET4000 VGA cards).
The Mega STe had a funkier case, VMEbus, and upgraded specs, but mushy rubber dome keyboard, more brittle plastics.
I like to collect the Mega as the best of the bunch, personally.