IMO, if MA was an issue you would have seen an initial slow down.
Use Onyx or another utility to clean caches, perform routine maintenance, delete Safari icon files etc.
I had issues on my Mac Pro when using MA to move from a G5. I did lots of house cleaning, including rebuilding the Spotlight index, rebuilding the Locate database, repairing symbolic links etc, Zapping the PRAM (which AppleCare recommended) etc.
Something I did "fixed" the performance issues and all I used was Onyx and Tiger Cache Cleaner.
I also agree that 1GB is a minimum for RAM.
Sorry for the somewhat vague "fix" suggestion, but I doubt MA is the culprit if the machine ran well initially.
Are only certain applications slow ?