The Legend of Zelda: Majora's Mask takes some time to get into, mainly because you're in that Deku Scrub form. It helps the first time around because you're exploring, but upon repeated gameplay it just becomes slow.
Chrono Trigger also takes a while to get into, but the plus side to this is for the first part of the game, you're at a fair so there is a lot of fun things for you to do and NPC dialogue which is actually... INTERESTING?
Parasite Eve takes A LONG TIME to get into. However if you can appreciate the story and the combat then you're good to go. Still it is a bit more realistic than other video games, some would say that this is one of its downfalls while others will praise it for this.
All Pokemon Games and I mean all of them! Even the spin-off games take some time to get into. It is one thing that I liked the original Pokemon Gold and Crystal over Pokemon HeartGold. HeartGold just wastes your fucking time. I know that a tutorial needs to be given, but damn does this take up way more time than it used to.