My preference on most stock is generally for an airline (window seat preferably) to avoid the risk of playing 'footsie' with a person opposite at a table. It especially doesn't help when people think it's acceptable to plonk their bag by their feet encroaching into the legroom of the person opposite!
It also reduces the risk that some oik has had their dirty trainers up on that seat previously.
However, on the Chiltern Mk3s, most of the airline seats have been replaced with newer 'disabled friendly' seats, which I find much less comfortable, so tend to opt for a table with the old style seats instead.
Like most have suggested above, I'll go for a table window seat, if the opposite window seat is unoccupied.
The situation I dislike most is when the only available option is a table with one other person already sat in a window seat, and you know the train is likely to get busy.
You can either:
a) Sit directly opposite them in the other window seat, and risk playing footside, which can look a bit odd, but at least you know you won't get disturbed later by other passengers taking the aisle seats.
b) Sit diagonally opposite in the aisle seat, but then can't relax too much because when the train gets busy, you 'll have to either shuffle across to the window seat or get up and let someone into the window seat.
It's also a difficult call to work out if/when to move pre-emptively as the train starts filling up, so you don't look like a jerk trying to block the window seat!
Don't get me started on people who sit in an aisle seat on a busy train, then fill up the window seat with all their stuff to try and 'block' it. I am very good at saying "Is that seat taken" in a way that strongly implies that they'd better move it or else!