So one person thinks Tioga Pass is just fine, and another considers it RV-unfriendly. What's the point in asking about best routes, if posters can't agree? :)
The route from 99 takes you through the Sierra foothills and valleys to Yosemite Valley, which is what most visitors come to see.
The route from 395 climbs to the park entrance station at Tioga Pass, the crest of the Sierra Mtns. It then crosses Yosemite high country before winding down to the Valley.
You could, of course go in one way, and out the other. Or go in from the west, and take the toad/tow up to the high country.