I say you focus on a few of your favourite systems primarily. make lists of games you want and slowly work on that, then move on to other systems when the pickings are either too slim, or too expensive.
alternatively, you could make a list of top 10 WTB games for each of your systems and cross them off when you get them, this way your collection will grow more evenly?
I have a collection of 3000+ games, over half of that is NES, Atari 2600, and PS2. most other systems I'm very picky about what goes into it as I've run out of space. I have plans to fix that but until then I
I recommend not buying bad games to fill your collection, and also recommend not trying to get all games for any system. IMO, they are a waste of time/space/money and eventually you will just want to get rid of the stinkers because you won't ever play them. I still have a bunch in my collection, but in my own defence, I started collecting in 1999 when it was so much easier to find anything in the wild for next to nothing.
be selective and buy the stuff you know you will enjoy. but ultimately, it is your collection, enjoy it and build/destroy it however you please!