The Midland Junior Premier League was set up in 2004 with the intention to bridge the gap between academy and grassroots football - it had age group teams from U12-U16 for many of the biggest non league teams in the Midlands, and clubs who were successful in their local leagues were often encouraged to enter the League to play against the best teams in the Midlands, so to speak. Up until 2011, the MJPL operated and featured these big clubs from the Midlands but then there came a number of issues if I remember rightly - their website was shut down, there were concerns about the standard of the league (e.g. big scoreline differences like 10-0 victories were quite common, and it was believed that this was because too many clubs, playing under the banner of a professional club , were not actually that good).
So then some of the managers from the Midland Junior Premier League (I think Bath City in particular were involved in this) decided to create a new elite league which they originally named the Junior Premier League South', featuring many of the teams from the MJPL but also quite a few more teams from the the Somerset area going all the way down to Bournemouth. Over the years, the Junior Premier League expanded and thus were able to drop the 'South' from their name (I think in 2013) and now there are leagues within the JPL covering all parts of the country, whereas the MJPL still covers the Midlands area only.
The website of the JPL seems to be a lot fancier that that of the MJPL, and I think it's because there are so many more teams serving as feeder/shadow teamas to professional clubs in that league. As for comparisons about the standards between the leagues, it is probably the case that one can only really compare the standard within the Midlands for a fair comparison, and this is hard to deduce because for all the glamour of the JPL's website, it says relatively little about how good their players are compared to the MJPL.