All of the advice I have read on this site says to play with 100bb min and have auto top off turned on to get the maximum value out of monster hands. Would it then be -EV to have the largest stack at the table considering you can never double up, therefore never winning 100% of your stack size? For example at a .02/.05 table if you have $5.00 and someone has you covered on an all in with $6.50, you win $5.00 or 100% of your stack. In this same situation if you have $10.00 and win you only win $6.50 or 65% of your stack. I know it may be a totally different situation, but it seems to me that once you have the largest stack it is no different than sitting down with 100bb at a table of SS'ers, minus the SS strategy.

My question is, do you leave once you have the largest stack? (obviously assuming it is an average table, not a ton of fish)

That doesn't make any sense, you are thinking about it totally wrong.

Think about it this way, one way you can with his $5, the other way you can win his $6.50. There's nothing else to it, bigger is better, unless you are poor at very deepstacked play.

The only time I sit up and leave is if a smart aggressive opponent has position on me and we are super deep - I don't like my edge in these games too frequently and will sit up. Otherwise, I just let it grow and grow.

Yeah you are not thinking this through. If the 2nd largest stack on that .02/.05 table is $4, it doesn't matter if you have $5, $11, or $1,000,000. Any amount over the 2nd largest stack is not at risk, but you have the potential to maximize your profit as long as you have everyone covered.

I always want to be the largest stack at the table - no matter how many times I have to double up to get there.

You are missing a big point here. You don't leave because of your stack size. You leave when you no longer have a significant edge (at an average 5nl table, you should have a significant edge).

Also, let us imagine this scenario. You are at 5NL with $10.00. The fish on your right has $5.00. Next hand, he doubles up by hitting a miracle 3 outer on some other player. You are now 200BB deep with a fish on your right. Next hand, he limp calls your raise (you have AKs). You flop the nut flush when he flops a worse flush. You now stack him for 200bbs.

Let that sink in.

You are indeed thinking about it wrong.

But you hit on a very important point about stack management.

If you are deep and the only players you are deep with are better than you or = and very aggressive with direct position on you.
Chipping down if allowed or changing tables is advised.

Being as deep as possible is not always the most +EV decision.