Wow - if border security relies on stamps in passports we're all in big trouble...
The only countries that "cause problems" due to stamps in passports are not exactly the world's most developed/open countries anyway - but they are places where a lot of us have to travel to for business, so we go anyway (or change jobs).
It takes at least one week to get a Russian visa (and often a lot longer), Same for Saudi and many others, are you suggesting that very frequent travellers (like most of us) stop travelling, for a week or more whilst we get a Visa? Not possible.
As for travelling to ISIS areas - I have 6 trips to Turkey so far this year- one of them (this week actually) was to an area about 50km from ISIS (and an area of Turkey with an uncomfortable ISIS presence), however the stamp in my passport from that trip from Ataturk airport looked just like all the others...
I suspect that terrorists don't fly directly out of Peshawar and Drug Smugglers directly from Medellin.