I agree with you, heck, I support a mid-table League Two team. If the proposal means that there are suddenly 20 new B teams flooding into the league system (which I'm concerned it does) then there's a problem. But if it's just say the big five teams (Arsenal, Chelsea, City, Utd, 'Pool) putting out B teams, then I think it's an overreaction to say that it's going to spoil the heritage or opportunities of any of the 72 clubs currently in the Football League.
If anything it could help enhance the Football League if these B teams play in their parent club's stadium, imagine being an Exeter City or something and you get a day out at Old Trafford or Anfield, with a bigger crowd than you could ever expect to see at a normal League Two match. You might also be able to get to see PL stars playing against your club from time to time as well, if it's allowed. That normally only happens if you make it to the 3rd round of the Cup!
I actually disagree with this. I think it would weaken the competition at League Two and League One level, not strengthen it.
I'm not sure why you'd swap out a current League Two side for Chelsea reserves. How many people are you expecting to watch these B sides? Barca B play infront of no more than 2-3,000 home fans, don't they? Madrid even less? How many are you expecting to be at Stamford Bridge? How many are you expecting to make the return journey at your home game? And which clubs from League Two right now are you throwing under the bus to make this happen on the basis of an off chance that a half-established player turns up for 60 minutes? Burton Albion? York? Exeter? Wycombe? Plymouth? Portsmouth?
You're swapping out proper clubs at a competetive level of the game, competing with each other for genuine progression up the football league, in favour of pointless games in empty stadiums and away ends for the benefit of the Premier League.