I have been investing most of the legos in various themes with Star Wars being about 30% and the largest in my inventory. Now, With $2000 to invest. Would it be better to invest in modular s (fire brigade, town hall, grand emporium etc.) or other themes as hobbit, more star wars, Super heroes and LOTR or other themes. Just looking for about a year worth to recoup or max 2 years.

Diversify........buy some of each, no need to sink all $2,000 into one theme.

1-2 years I wouldn't be looking at modulars

Avoid modulars if your investment horizon is 1year with 2 years as a max. Look at the first wave of LOTR or Monster Fighters which are both imminently EOL, or wait a few months and grab some of the other 2013 sets as thy go on sale leading up to Christmas. Sell next fall before Christmas 2014 to maximize profits. Wash, rinse, repeat.

In two years the GE and TH could be golden......

Buy 1 of each Modulars available (try to hit 5% discount atleast) and buy Monster Fighters/LOTR/Hobbit/some cheap city sets (anything on 30%+ discount might do good 2 years after EOL)

I'd advise you to look at set like Haunted House, Bag End, Sopwith Camel, Tower Bridge, VW Camper, and maybe some trains or larger Friends sets.