I actually used most of the Pok?mon given to you as you progress through the game. I just feel bad when a Pok?mon asks to come along with me, and I just transfer it straight to a box haha.
By the end of Y I was travelling with Delphox (A fire-fox-witch suited the magical feel of the game (in terms of colour and design, music and sound effects) perfectly), Venusaur (because Bulbasaur is my favourite Gen 1 starter), the Snorlax you wake up on Route 6/7, the Lucario that befriends you, Swanna (mainly for HM moves - and I found Surf and Fly really useful in battle too), and then I think my sixth slot was just used to evolve other Pok?mon.
I didn't realise you could get a Lapras from an NPC until after I had finished the game (much to my dismay, because it looks so cool riding on its back while using surf).
I bonded with Delphox and Lucario so much that they are in my party in Moon at the moment.