Music notation and MIDI are not equivalent
Although, to a beginner, it is helpful to see the similarity between notated music and MIDI as opposed to sampled audio, such as wav and mp3, differences start to matter once you start making music.
Nuisances not expressed in notation
Even if software may successfully convert from one to the other, MIDI, just like human players, does not have to strictly follow the notated music. One ordinary example is MIDI created by recording real time performance. Unless you’re a robot, this will normally look like a mess when imported to many score editors [http://www.skytopia.com/project/articles/notation.html ]. Playing “perfectly” as notated, is not very expressive. Whether one can play “perfectly” or not, one would likely add nuances and “feelings”, playing notes a little earlier or later, or shorter or longer, or louder or softer, than what notation indicates.
A direct MIDI export from many notation editors (e.g. MuseScore), will give an unnaturally clean and “perfect” sounding output. Many of the processes of “MIDI orchestration” or “humanizing” deals with correcting the transition from a printable readable score into a MIDI arrangement to trigger samples in a DAW.
Piano roll vs notation
At first, I exclusively used notation because of how it enhances your, “ahem,” notation skills Notation has it strengths being compact (a whole note is not drawn four times bigger than a quarter note), legible (16th notes are not 16 times smaller, likewise), and standard. The main issue for me is the work flow. Starting notation from scratch enforces quantization and strict rules. Frequently, when starting from scratch, it is tedious to adjust note positions and lengths to get a measure sounding the way you want it to sound (which is most likely filled with nuances). I think I can only reliably notate up to quarter notes, then the smaller ones are trial and error. This trial and error procedure takes long if your notation editor takes many little steps to put notes in place.
Imagine moving a quarter note back in time by 1/16th of a note. One way to do it in a notation editor is to trim off the note or rest before it by 1/16th, delete the note to be moved,then making one in the new position. Whereas some editors allow dragging notes horizontally in time, adjusting the rests surrounding it, this approach is still constrained and a bit tedious if there are already surrounding notes. Not surprisingly, a piano roll editor that only sticks to notation-like quantization/snapping to grid can also be a headache. Although quantized MIDI is good if you eventually want to convert to notation.
Another complexity in notation is voices (not to be confused with the human voice or instrumental timbre). What are voices? Imagine your right hand is on a piano keyboard. Each finger may play different notes at the same time, for the same duration, forming a chord. But it is also easy for each finger to play independently. So your thumb may play a whole note, and while that whole note is playing your index finger plays a succession of four quarter notes. How to notate this is seldom explained in beginner books as it may be confusing to look at, appearing to violate the conservation of time. In music notation software, voices are treated like layers in graphics software like Photoshop or GIMP. It will take several mouse clicks to go from one layer to another. In a piano roll interface, there is no concept of voices, making such note entry simpler.
So in the end, I gave up trying to create a nice looking sheet music and edited freely via piano roll, adjusting notes little by little until they sounded right together. This means that you should choose a MIDI editor that can break away from quantizing or snapping to the time grid. Good piano roll editors have the feel of MS Powerpoint or Inkscape vector graphics editor, wherein resizing or moving shapes is straightforward dragging. As we are more perceptive to when a note starts, you would likely focus on the left side (note on) part of the note. Actually, I feel that my ears became a little sharper after editing MIDI this way.
A free MIDI editor I tried that can do this is Sekaiju (which I plan to review some time). It has it’s many quirks, but is quite powerful once you get the hang of it.