I think they all have more or less the same area, so it depends more on the most practical shape. Concordantly, while some may appear to have larger areas, they actually have about the same area as the smallest bases, just arranged differently.
What you want is a short, wide room instead of a long, narrow one. The one on the route east from Fortree City has probably the best internal arrangement, and it also exists in the area north-west of Fortree, just it's not really accessed easily.
Have a look around, and choose the one which will be most practical.
yep. the bases around fortree are huge. your best bet is one of them.
It seems that this base on Route 120, and this base on Route 119 are the roomiest ones on the map. There are many similar bases like this throughout Hoenn on Route 118, Route 115, Route 111, etc. You can visually look through all the secret bases on those links and see which one fits the best for you.
Hope this helps!
