it is not improving Con because you get extra FP per point of Con above 5. No one takes Con below 5 because it means low hp and PhysRes. Everyone places Con 5 and then have to decide whether to put some more in it or not. Your rule ststes that +5 Con means only +3 fatigue to spend instead of five.
No, because until 12 CON the penalties come either at the same or lower fatigue. This means someone putting 11 CON (and thus 11 Fatigue) is at equal ground to normal, 12 and higher it becomes a problem. So your complaint only applies to 12+. And not even all that well considering it only decreases the "usable fatigue" by 1 till 14, 2 by 16, then it becomes a problem 3 till 16 and 4 till 18 and 5 at 20 (assumed max see below). As noted above Tireless needs to be moded so it is still useful...or it did until,
you are assuming that con is the only way to gain Fatigue
In addition to the Tireless advantage, which grants 3 points of Fatigue, there is a stackable Gnosis 0 monster power for a measily 10 dp which adds 2 fatigue.
I did not know about this, and it never came up in game. However this makes my HOUSERULE become a problem for Monsters (which in and of itself is not a problem), but also players that want to use monster powers. If it just worked off CON (as I thought it did) + Tireless if wanted (and needing a change with Tireless), this would work albeit not perfectly.
Therefore you are correct I have to change my HOUSERULE. I still hate the official rule, so I will merely modify my HOUSERULE. I will just input those maximums (4/3/2/1/0) and use my original percentages otherwise (50/30/20/10/0%). This way increasing fatigue is useful, but people with little fatigue can use it without taking a penalty for using 1.