ok so I'm not going to go through over 100 pages to find this so excuse me up front.
Somewhere I read that you will get a much better beer out of the kit beer packs if you don't do as instructed and just toss the dry kit, yeast and water but go ahead and boil as you would with a normal DME/Mash recipe. Yes, no? If yes do you have a preferred boil time?
Like some others that have posted I'm just starting out although I stopped using the prepacked kits that came with this thing after the first batch of basically dullwiser. I'm about to bottle my Black Butte clone and have several more kits and thought I would go ahead and give it another shot vs. wasting them. Was hoping to bottle tomorrow but looks like I'm still fermenting after 3 weeks and I've keep the temp near perfect the entire time. Other than not drinking more than a few bottles a week so not needing 50 bottles or more taking up space aging the Mr. Beer and clones will fit inside a large cooler allowing you to really keep that temp where you want it no matter if the wife turns up the hear because she is cold plus if you have leakage it's contained.
The kits include hopped LME (HME in Mr Beer parlance). The hops in an HME have already been boiled at different times to provide bitterness, flavor and aroma. If you boil an HME, you'll move the aroma hops to flavor hops (and possibly to bittering hops if you boil long enough) and the flavor hops to bittering hops. So you'll completely change the character of the HME.
I'm not sure what you mean by tossing the dry kit, yeast and water.
You can use a different yeast if you want (I like US-05 or Nottingham in cooler weather for "clean" fermentation, for example). The yeast that comes with the kit is pretty tolerant of a wide temperature range, and that's why they use it.
You can certainly add more malt, either LME, DME, or, if you have the time, you can do a partial mash. If you add more malt, the beer will be sweeter unless you also do a hop boil. Boil the hops in the malt you add (use enough water for a gravity of about 1.030-1.040; if you don't have a hydrometer, use brewing software to estimate) and add the HME at flameout.