Actually, I think that you are doing something wrong, because I do not suffer from the same problem. I quote from a fine guide:
"Probably everyone, who played FM at least once faced a problem of bad physical condition of their players early in the season, especially the first one - when the players are very tired after the game and often get injured. The reason of all misfortunes, as usual, lies on the surface - pre-season training was unsuccessful. Actually how to prepare your team for games during the summer (or winter) break, will be discussed in this article."
Condition is a combined figure, equals to Fitness*86% + Match Exercise*14%
So, you might think that just having a good Fitness is enough and you don't need to worry too much about match exercise. But:
"...Fitness recovers better when value of Match Exercise is higher. Similarly players, who have low value of Match Exercise, get tired faster in matches and are more likely to become injured. That's where we face problems..."
Some suggestions:
"To get your team fully fit to the first official game, it is necessary:
1. That each player has played necessary amount of time in friendly matches. I have written formula above, but to make it easier I will say following. If player's Natural Fitness equals to 7 - 4 full matches are needed, if NF=17 - 3 matches will be enough. The rest - on a proportion. Thus the break between matches should not exceed 8 days.
2. To play last friendly 8 days before the official one. Then it is enough that player's fitness on the match end was not below 69% and condition below 73%. If it is 7 days before a match, fitness will have to be 79% and condition - 82%.
As a result the best schedule of friendly matches will look like this - last match 8 days before first official and 3 more matches with an interval in 7-8 days. If you for some reasons, don't have enough time, arrange the matches so that the interval between the first matches was less (e.g. you begin on 10th of July, so arrange the matches in following order 11,14,17 and 24th of July) - then Jadeness will be gathered in smaller portions for a match (as will not have time to fall) and when reaching the date of official game it will normally fall. While during first three matches players will have to play all 90 minutes, during the fourth one you will get an opportunity to regulate the amount of time spent on pitch so that everyone had enough time to get enough match practice and the condition level wouldn't fall lower than critical (condition is much more essential). Where and with whom to play isn't important. If to reject desire adjusting your tactic to ideal or to get as much money as possible while playing with "big", playing with your own reserve team is the best option. You will save the time, will be able to minimise risk of getting your players injured, and the main advantage is that 22 players will be used so you'll have 2 starting elevens in superb condition.
It doesn't mean that only this schedule is correct and it is necessary to play only this way. The main idea is that only three factors matter - total amount of minutes played (and it needs to be allocated more or less during pre-season period), the date of last friendly match and the condition level at the end of it."
You can make your own plans with this information, although I don't like this much micro-managerment, so I get a good Assistant Manager to arrange and take control of my friendlies. It helps if he likes to rotate the squad and use substitutes frequently, I think.