Unfortunately, quite often, they'd just drop randomly while you're hanging out on the ledge, and if you chose that moment to get off the ledge, dealing with the opponent pressuring you and trying to get away, you wouldn't be able to really squeeze the whistle in. Also, I found that quite often, Pikmin would just drop out after getting hit by a weaker attack like MK's Dtilt near the ledge, and then he might grab you or something while all your Pikmin randomly fall to your death. Although, yes, I whistle after DIing and all that, the Pikmins' tendency to separate from Olimar at almost random would be inexcusable with only three Pikmin. Not to mention that, as of the E3 build, Olimar's Whistle lost its armor, making it an actual risk to use.
Also, having three Pikmin is absolutely terrible. It greatly limits Pikmin Toss (even though it's been nerfed, too), puts a greater emphasis on whistle when Oli could be doing a myriad more relevant things, and generally puts Oli in a near constant "danger zone." When playing Brawl, whenever I see Oli with three or fewer Pikmin, I know that I need to pluck more because those three can be gone in an instant. Unfortunately, Smash 4 seems to keep the Pikmins' low stamina from Brawl, so a good deal more time is going to spent plucking than should be. One or two Pikmin dying in Brawl was essentially no big deal. Hell, even having only three would be okay for a couple seconds, as long as I could get the opponent off my back and pluck more. Here, losing one Pikmin is disastrous; losing two could severely cripple you, and at that point, you often don't have the momentum to safely pluck more, but unlike in Brawl where you'd still have four to rely on still, you only have one. With that one, you are forced to commit to any attack that you make to get the opponent away. One of Oli's big strengths is his lack of commitment to any one move because of low cool-down with the exception of the Pikmin themselves. If Oli does several Fsmashes in a row, you can see the Pikmin pile on top of each other because the first is still in lag while Oli is free to act. However, the more reliant on each individual Pikmin you are, the more this lag becomes evident, and with Smash 4 forcing only three Pikmin on us, Oli is going to have to commit a lot more than in Brawl.
Basically: three Pikmin means less options, more commitment with each individual move, and being forced to pluck more often in uncomfortable situations. The fixed order is nice, though.