It's not uncommon to have problems anytime they launch a new gen, give it a few model years for them to work out the kinks and you'll have a more reliable vehicle if your plan is to own it for the long haul.
Since it's been 10 years I'd say either way you'll enjoy being in a new car. If it were me, I'd wait for the 6th gen to come out, not because I want it but because that's when you'll likely find some really great deals on the current model year. Plus, if it turns out you really like the 6th gen...
If the resale value on the 4 Runner is your main issue then you might also want to consider that the SR5 will likely be an easier sell since it will appeal to a wider audience of buyers. This could be good or bad depending on the supply/demand at the time you choose to sell, but it will be...
Hopefully your dashboard lights don't stay on when your headlights are off or you'll be one of the guys I see driving around at night all the time with their headlights off!