I often have to upload the same sketch several times, for example when:
So it would be nice if a compiled sketch will not be compiled again if it is unchanged.
Just save the hex file.
The new IDE has already taken the compiling to a new level with a feature borrowed from the CREATE editor.
BTW tests on compile speed tend to favour the CREATE editor due to the fact that most of the work is done OUTSIDE your computers environment and unrestricted by your system.
If you are using the latest IDE just go to FILE and select PREFERENCES.
You will see an option called "Aggressively cache compiled core"
Enable that as it saves a lot of duplication in the compile process.
I certainly would not use the regular IDE for production runs of boards as there are far better tools out there for that aspect.
ALso ensure you antivirus / anti malware programs have the IDE components and locations WHITELISTED / EXCLUDED and you will also see an increase in compile speeds in order of magnitude.
You have over 124 posts but did not really provide much detail so that is the best I can give you otherwise I would simply have to guess and say you put the blue paint on backwards 
If you're doing production runs then just save the hex file and load it directly with AVRDude.
Or use a standalone tool like my programmer, put the hex file on SD card and just blast it onto your production cards
http://www.crossroadsfencing.com/BobuinoRev17/
