This past Saturday I experienced the joy of playing a huge 'company on company' (12 mechs vs 12 mechs) game of Classic BattleTech down at my FLGS. It was my first time playing on 3D terrain since my 6th edition Warhammer 40k days. I had a blast, but it reminded me why I was so happy when I learned BattleTech usually plays with hex maps instead of modeled terrain.
In my experience I have found that using measuring tape and eyeballing line of sight and cover allows a certain fudge factor to enter into the game. Hobbyist gamers tend towards the competitive side of the spectrum and I have seen plenty of arguments erupt over whether a base was just a hair out of range or not. Thankfully this past Saturday we didn't have any problems of this nature at our table and I got my first taste of combat using the non-hex miniatures rules.
In standard miniatures play each mech has its movement points (MP) converted to inches by doubling its value. If a mech has walking speed of 5MP it will be allowed to walk 10 inches on the table.
The GM running the game determined that we would be using a house rule where 1MP = 1 inch. This made our mechs less maneuverable than they would typically be in this kind of game. I suspect this restriction was put in place to compensate for the table size we had compared to the number of mechs in play. In a game with 24 mechs on a 6'x4' table managing combat between 6 players is hard enough without everyone zipping all over the map. As a frequent GM myself I respect that choice.
I point out this house rules change because my conclusions about tabletop vs hex rules might be biased based on how this house rule impacted the game.
There is a higher level of density and variety to the terrain on hex maps produced by Catalyst Game Labs for BattleTech that I don't believe can be produced easily with 3D terrain. The amount of tactical choices to be made for a unit moving on a hex map is greater than the choices presented to the same mech playing with the miniatures rules. This is simply a matter of how map design works between the two 'engines'.
3D terrain is limited by the real world physical properties of what you're using to build it. Light woods and heavy woods need to be a certain thickness to block line of sight or provide cover. Buildings must have a realistic footprint in relation to the roads, trees, etc. To a certain extent scale must be preserved across your terrain.
The scale of the hex maps doesn't have this constraint and as a result terrain feels more "gamey". River hexes can wind tightly around building hexes placed next to deep canyons, all within a few movement points of each other. Replicating the same setup in 3D terrain could be a month long project that may not in the end provide the same level of tactics as the hexes.
I'm not 100% sure on this hypothesis but it is my gut reaction after playing a game with admittedly weird house rules. In the future I plan on comparing 3D terrain pieces to their equivelant hex map setups and seeing the difference to actual play in the future.