The problem is the processor. On my laptop I have 2.7 GHz and it will take about 7-10 minutes to load 1,344 chars. On my Surface Pro I have 3.5 GHz and it takes about 1 minute to load 1,344 chars.
So basically you only have 3 real options:
1) Get a better processor
2) Use less characters
3) Go make a sandwich and wait 25 minutes to play.
Back in 2007 I was big on option 3. A fighting game with 1,000 to 3,000 chars is worth playing, even if it's huge!
Also!!!
You can also affect your load time by changing setting the data/mugen.cfg file.
Under the heading [Misc] you can change the parameters of "Playercache", "precache", "bufferread" and "unloadsystem" which will directly affect memory. In your case maybe turn off "precache",
I have never found this to make a big difference though.