I'll relay what I know on the subject which admittedly isnt much...
AFAIK, seb chips are piggybacked onto the original engine management, and change the various timings and settings a bit, but doesnt COMPLETELY change the mapping... so while they still do the job and are EXTREMELY good value for money, it's not technically the "best" possible solution to the problem.
Getting a standalone engine management system (is megasquirt one?) means you can hook right into the engine and muck about with settings to your hearts desire. This means essentially that you can do with the engine what you want - you can optimise it for absolute best possible fuel economy, or max possible power production all through the rev range (at the expense of your MPG rating..!), or leave it somewhere in the middle, jack of all trades, which is sorta how it comes from the factory. Or you can go for any point in between.
However its not something to be taken on lightly, you will either need to know EXACTLY what you're doing or be willing to pay someone who does - its not just a button you can press called "make car fast". If you try it yourself and muck up some of the numbers you could do some SERIOUS damage to the engine.