Stacking is a must for the game. You can give an option to disable that in the race menu, so those that don't like it won't use it. But it adds a lot of depth to the gameplay and makes it a lot more interesting.
As to the issue of the leader stacking... true, but the last place usually also will have an easier time stacking and since last place (when there are at least 6 players) gets Assassins almost insta-mode, stacking them up to a point where the 1st player will be blown into the outer space regardless of the level of his shield is essentially a perfect counter for that. I honestly think that stacking would help with the issue of 1st player running away, rather than making it worse.
Naturally the pickups will have to be balanced accordingly, so it's worth waiting when you have an opportunity, but not so much that you won't use it when you have someone in front of you waiting to be blown away. That said it shouldn't be as difficult to balance as some other things, namely...
... 3rd pickup slot. That is just a no-no, since pickup stealing is already an issue and the main reason why 1st player can actually run away. If you have 3 pickup slots, add to that stacking and you have potential of taking 6 pickups without dropping a single one. That's pretty much the amount of pickups most people get on average on a whole lap. With 2, you can only steal 4 pickups and the chances you'll even be able to steal them are lower, since you can only have 2 different pickups, not 3. So we have an exponential growth here, not linear.
So it's either 3rd pickup slot on all cars or pickups stacking. But with the current amount of pickups on the track aka barely having a single one when having another player nearby, 3rd pickup slot could only strengthen the "1st player running away" issue without providing any countermeasure. Currently pretty much the only time you really wish you had a 3rd pickup slot is when you're... 1st.