Hi Jovin,
As far as I know, there's no way to speed up the calculation without sacrificing quality. However, if you're willing to sacrifice
some quality, then set the 'nIter' parameter in the
water-table flooding wizard to 2, or even 1 (the default is 3, I think). This reduces the number of iterations the calculation will perform, so if you're unlucky (i.e. your map topography is complex) the final result will be less smooth and might look odd in places. However, it's generally safe to use an
nIter of 2 on most maps.
Your other option, which I generally don't recommend, is to skip the water table altogether. The water-table is basically used to get slightly prettier texture/land type positioning for such things as mud/sand near water, greener valleys, barren hill-tops, etc. In circumstances where the only water bodies in your map are at 0m altitude (i.e. no 'auto lakes'), this can work OK, but you need to use a climate optimised to work without the water table. 'Temperate (basic)' is an example of such a climate. Nevertheless, the textures produced by this method aren't quite as pretty, and you'll also need to spend a lot of time messing around in the climate editor tuning the parameters and altitude ranges to get things to look right. Not for the faint of heart.
Oh, one last thing. The estimated time remaining that's displayed for the water-table flooding calculation grossly overestimates the time at the beginning (maybe by as much as 3x, according to a quick test). So if it says "2 days" initially, it doesn't really mean it. The reason for this inaccuracy is that the water-flooding algorithm does some self-optimisation that kicks-in after a few cycles and speeds the whole thing up. This optimisation is dependent on both the map and the settings chosen by the user, so it can't be predicted in advance.
Cheers,
Aaron.