There are numerous rules in MLB regarding roster changes that really can't be implemented here because of practical reasons.

You have pointed out one of the issues that works to hurt a team.

Let me point out two of the ways in which Purebaseball is different from MLB that helps a team.

(1) Unlimited Moves Every 5 days.

In MLB when a player goes down to the minors they cannot come back for 10 days unless another player on the team is injured. In Purebaseball you can send players up and down as much as you want between series. Suppose you wanted a 5 man pitching rotation but only wanted to use 4 roster spots for the pitchers. You could do something like this:

Series #1:

Pitcher A
Pitcher B
Pitcher C
Pitcher D
Pitcher A

Series #2

Pitcher E
Pitcher B
Pitcher C
Pitcher D
Pitcher E

Another example: Suppose your team faces a team this week with no lefty pitchers. You send down all your hitters that bash lefties and bring up someone else that can help that week. Then after 5 days you bring them back. In MLB you have to leave them down for 10 days.

The second major restriction that MLB teams have is that (uninjured) players with a certain amount of experience cannot be sent down without clearing waivers and/or consenting to be sent down. So if you are the Los Angeles Dodgers and Eric Karros stinks this year you cannot send him down unless you risk losing him. If you are a purebaseball manager you can send him down, insert someone else at 1B, and still hold Karros for a chance he could be better next year.

All in all I think when you compare the PROS of the current system (added flexibility not present in MLB) with the CONS (once in a blue moon someone gets the injury shaft) I think the system is ok.