"And in some cases (see above) make someone in the future go mad. An ISR that depend on no other ISR being less than 250 cycles is a tickin time bomb"

Solution 1: Make the timer interrupt the highest priority.

Solution 2: Comment your code.

250 instruction cycles at 3.3864MHz on a 12 clock device takes about a millisecond. To put this in perspective, you'd be starting to have trouble receiving data at 9600 baud if your serial interrupt was not the highest priority one in the system and you had another ISR that took more than 250 instruction cycles. You wouldn't argue that you shouldn't use serial comms in this situation, would you?