First of all when considering SW I would most definitely point you toward keeping CAD and CAE tools separate. I don't have a problem with SW producing the "swoopy" shapes needed for aircraft or most anything else. Salvador, Eaton, Wilson and others have gotten extremely good results out of SW in that area. I have to ask how large your assemblies may get.
In the area of interoperability with imported geometry you will probably have some concerns. SW just doesn't go the whole 100 yards in this area. But there are addins or better, standalone packages from places like Capvidia that can do an outstanding job of getting you past this hurdle.
I mentioned in the beginning standalone CAE tools. I am not a big fan of integrated tools. Documentation of models is one big issue I have. If you know FEA you know that the results are good for the geometry used at the time of analysis. It is all too easy to change the model after an FEA run and lose the geometry. For that reason I prefer products like DesignStar, Cosmos/M, NEiWorks and NE Nastran. When you do the analysis you also get a file (either text or binary) that contains the geometry you analyzed. It can be archived will little change of inadvertent changes. In addition, standalones don't tie up a seat of SW while running. I have used all the products I have just listed. Also, standalone may give you economies of networking fewer licenses.
You can't beat Nastran for modal analysis and if you go with NE/Nastran you can do structural, thermal and they even have a flow package, though I haven't used it. NE/Nastran uses the FEMAP preprocessor which is a bit antiquated, but very capable.
In addition for CFD I use CFDesigner. I have also used FloWorks, but I prefer CFDesigner and own a seat.