Just chiming in to say that this is the first thing that I ran into while reading the changelog for 5.4. I use this exact approach all the time.
In some cases, I can easily switch to making factories:
$something = app('some-factory')->make('object', ['param1', 'param2']);
In other cases, I'm not so sure that is a practicable approach.
I'm half considering writing a package that brings back the old App::make behaviour in a separate stateful 'container', just to make the transition easier.
Though long story short, I haven't decided either, yet, how to tackle this.
In any case, removing this IMHO pretty crucial bit of functionality with minimal explanation (just saying it has a code smell is rarely justification for making a pretty big breaking change) is a bit of a shock. I'm ready to learn what is so terrible about binding interfaces in the container this way, but it deserves a bit more than 3 short sentences in an upgrade guide... :]