I enjoyed having a Pokemon follow me, but I can see why that was removed. Think about it this way: Imagine if you were a NPC in the game and this kid with a huge Legendary Pokemon was walking around a city like nothing was going on. I'd walk around with Lugia or Groudon following me in SoulSilver and think "I wonder if any of these people are even concerned that THIS Pokemon is roaming around in their city!" Looking at it from that world, people would freak out if a Legendary Pokemon was just walking around in the middle of the day!
If that would be main matter, this feature would be never created in HG/SS. Also, you can still use legendary Pokemon in battle against ordinary trainers with weak Pokemon and nobody freaks out.
I think this feature as well as running without holding button was removed in B/W to make comeback in B2/W2 or/and R/S remakes to make people more interested about those games.