"Best" is too broad for a poll. Best architecture ? Best gameplay ? Best balance ? Best for aliens or for humans ?...
Nicest looking has to be Karith. It would be the best gameplay wise if not for that evil elevator room...
Transit features an unique gameplay , but egg hunts can be tedious. Jetpack is rather powerful here but remains counterable anywhere (thanks to ceilings)
Arachnid2 is also very nice. However a large part of its eye-candy impairs alien movement , especially wallrunning - it is most disorienting on this map , and unfairly so when humans can attack the default alien base from over the pipes.
Actually Nexus6 suffers from the same problem - many surfaces unclimbable , such as the griders blocking the human base corridor's ceiling. The tight doors are rather annoying for large aliens. Otherwise , a fun and balanced map.