I think that it is totally intended that farming plots take up a 3x3 space physically but visually only look like a 2x2 space. I think this is intended so there is an aesthetic path between the hedges crops.
I did not notice the reduction in town size, good catch.
I actually very much dislike the restriction of road only on the outer edge of Syndesia towns as I would rather place crops or houses there and a supporting ring of road further inside.
However. I do believe that the reduction of the size is intended to reflect the reduced need of space that Tera has for it's towns due to no need or use for a prison or siege workshop... It would be nice if we had some other specialty shops for Arborious which would then justify the larger area.
While the road bug does make city planning a fun game of Tetris, I think it is certainly not intended. I also would agree that a 42x42 space would be considerate once the bug is fixed such that there is space for buildings, roads, crops and the aesthetically lovely huge trees and boulders (which I feel we should be forced to build around and not able to place things over).
The house issue is a real bother. I accommodate by placing 3 of the 2x2 houses on a 5x5 plot, but even then the game wont let me place more than two furniture pieces (workstation/chest/bed/fire) in each 2x2 house despite there being room (reported). It would be nice to get the 3x5 T.
It will be interesting to see how the 3rd crop will effect space demands on towns and I expect it to become quite the bother unless veggies/leafy greens nicely replenish legume nutrients.
Jacopo has repeatedly said that the intent is that you can either have a self sustaining town or a dependent city. He even gave the example that a rank 15 city should need the support of two farming towns (or sufficient raiding income) to sustain itself.... This may be enforced either by increasing the prestige needs such that a town has to be full of buildings to reach the target, and thus no room for crops, or to increase the crop need such that there is a steep tradeoff up to rank 10, or simply limiting the space available such that you cant have both.
My guess is that Myr was on the small side, Aerhen on the large side, and Tera somewhere in between. At launch we may find that this is all just them testing to see what size is best and have all towns follow that format.
My ideal city would be on the large side, with optional wall, obstructing aesthetic elements (ponds in Myr, giant trees in tera, lava pits in Tartarus, and big boulders in Aerhen) for character, and no requirement to put a road where the wall meets the town.
In my opinion the biggest issue that you mention is the fact that there is no way for a house plot inside a town to be removed other than by the owner... This could very well create a town full of dead residences. I urge the Devs to apply some insubstantial rent on these plots (say 10g/week) and a modest cap (say, 2 month supply) such that extended absences can be cleaned up and more active players can take the space.