Question: I'm a self-taught hobby pianist with small hands, which means that often I need to substitute notes to be able to play something comfortably (or at all).

E.g. in Traumerei, there is a 10-note reach for both hands in the 3rd-to-last bar. At this point in the score it seems (to me at least) that the composer aims for a certain fullness in the chords that seems impossible to get by dropping any of the existing notes. By re-assigning which hand plays which notes (and keeping the top and bottom the same), I came up with the following (which sounds ok to me):
![chord substitution in Traumerei](https://i.stack.imgur.com/2Gtar.png)

For the second to last bar in Chopin's Prelude in E-minor, the first chord is only an octave, but I haven't found any fingering that isn't painful. The substitution I've made sounds good to me, but is the result of trial-and-error (and I'm not even sure which chord it is..)
![chord substitution Opus 28 no 4](https://i.stack.imgur.com/vFVCJ.png)

Are these substitutions reasonable? Is there any procedure to follow to find substitutions that doesn't involve as much trial-and-error? (after a while everything starts to sound "wrong"..)

Answer: 
The first one's OK, you've redistributed the original notes. But in the second one you've invented a new harmony, and that ISN'T OK! I suggest you simply leave out the low E in the RH. Or even play the B octave a bit early, catch it with the pedal and take the E with your LH.
As a supplement to @LaurencePayne's answer:

For the first chord, have you tried playing both lower notes, the F and G, with your thumb? If not, give it a try; perhaps it will allow you to play as written.

Regarding the second chord, dropping the low E is the best option, because that pitch is doubled by the more important E an octave higher.