The Trainer manning the gate glances around the compound and then looks at the queue behind you, you've got a few moments before the next trainer arrives. "Security." He says flatly, then says in a gentler tone "It hasn't happened since The Giovanni Incident, but criminals, Team Rocket in particular, used to regularly take a crack at Oak's lab. Especially when we were sending off new trainers."
Spoiler: Perception/General Edu results
Now that the Trainer has mentioned it, you can't help but notice the increased security - you can see several trainers loitering around key areas of the compound, watching the skies and the incoming trainers closely. None of them stand out to you.
When you reach the clump of trainers and researchers at the door, it becomes apparent that people are being sorted. There are a handful of researchers with clipboards talking quietly with the assembled trainers, occasionally calling out a name over the conversation. The other researchers are leading small groups of trainers into the building where they quickly disappear down a hallway or through a door. It would seem that trainers are being sorted based on if they need to be given a starter and pokedex, need to register a Pokemon and receive a pokedex, or just need to acquire a pokedex as they have a registered pokemon already.
Since your pokemon was a gift, it probably hasn't been registered to you, and you need a pokedex from Professor Oak.