That's short sighted because there is a development point of view for having the MwBoS, and that is introducing a faction that is fresh and neutral. What does this do?
1) Fo3 players won't feel tied to the new faction. If it's the Lyon's brotherhood, people will feel compelled to join up with them due to rosy retrospection from Fo3. The other factions may have good reasons for joining them, but there will exist that tugging feeling to join the BoS. Same thing happened with the Imperial Legion vs Stormcloaks.
2) There's potential set up for the MwBoS to possibly clash with the CwBoS in a future title. An eastern counterpart to the Bear vs Bull debacle over in the West.
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They don't have an issue with introducing new factions. Do you think people were extremely confused over the fact that the Mage's guild or the Fighter's guild didn't make an appearance in Skyrim? They replaced them with two new guilds. The Brotherhood of Steel is still the Brotherhood of Steel - they're just composed of a few splinter factions that think they're special snowflakes. They all tip toe along the same line in the sand.
I don't mind suspending my belief in the name of developing a fun and enjoyable environment. I make that sacrifice when I see a companion waltz up after being riddled with bullet (which I prefer), or how jamming 50 stimpaks into your chest cavity can mend the broken bones, bullet holes, and 3rd degree burns you suffered from the recent battle.
But as far as story goes, and from what we all DO know about the CwBoS, them magically appearing with an advanced airship contradicts EVERYTHING they were up to at the end of Broken Steel. Beginning with the mangled state they were in and ending with their vested interest in rebuilding Liberty Prime with iterations on the old design - unless the poor LW was wasting his time turning in all those lightbulbs and fission batteries and better off selling them - poor bastard.