No - it doesn't MIDI files don't sound like anything at all - it's the same as the lighting guys saying their DMX looks good or bad, when MIDI, DMX and other protocols are just information. Why are you creating MIDI files? You mean you are creating backing tracks that sound good on your system but sound poor when that audio is played on a PA?
The mix should be the mix. If you are using MIDI to drive external synths rather than internal VSTi sounds, then presumably you then route these synths back to the cubase input and record them?
What comes out of your studio speakers should be the same as the PA - unless the PA has an extended bass response your studio monitors don't - but this is easy to check. Take a well known - full bandwidth commercial music track - something with proper bass at the bottom, male or female vocals in the middle and lots of cymbals sizzling at the top and play this on the PA. Does this too sound weak and too bassy?
If it does, then it's just that the two speaker systems reveal and hide things from each other.
MIDI files rely totally on the equipment you play them on - so are you using the same MIDI source at the gig? If you use a Yamaha MIDI device in your studio and a Roland at the gig, they will always sound different. However - you said you 'convert' them to audio? In ,my studio we work lots with tracks and we never create MIDI files and we never have to convert anything - we simply hit record and play the master keyboard - the music might come from external synths playing via MIDI, or might be using a VSTi - and often both. MIDI just describes the interface between the kit - it's totally non-exciting and is just a protocol for which note, when and how loud in the main.
Can you explain a bit more your workflow - what you are doing - how it is connected, what the converting you mention is all about? I cannot visualise what you are doing. I can't quite see why you are trying to create MIDI files at all - the usual cubase file type can deal with audio and data. Exporting a MIDI file is a really rare thing for me - I've no need for them at all. For me, everything ends up as .wav files, or mp3s.