Couple of observations.......
Two smaller tanks wont necessarily be cheaper than one big one.
However if given a choice of a 90 gallon reef and 300+ FO, or a 180 reef and a 180 FO, I'd go w/ the two 180's.
I'm still assuming you could use one room as a fish/mechanical room to house all of your pumps, skimmers, sumps, etc....
I'm a big proponent of using the biggest freakin skimmer possible.
This website has a good explantion of how to figure out what size skimmer you need.
http://www.superskimmer.com/Display%20Tank%20ETSS.htm
F/O tanks tend to run dirtier, than reefs, but the occupants are much more able to tolerate the conditions than the reef will also.
Do you have a scientific name for the white spot grouper? Thats the only one that can be a problem in your system as many groupers will reach very large size in a short amount of time. I reccomend Scott W. Michael's books "Reef Fishes", for fish husbandry and captivity requirements. His 2nd book in the series, "Basslets, Dottybacks, & Hawkfishes" has its entire first chapter devoted to groupers....good reference books for anyone.
Finally, I also agree w/ MPS5906 on having two seperate systems as opposed to one large combined system, Unless you went BB on both and got an obnoxiously large skimmer and really kept up on your maintenance. More moeny to keep em seperate, but much less hassle IMO...
Nick