You sure it was easier? Barcelona did score 114 goals last season in the league. On average it might have been but perhaps not in relevance to their respected teams.
Well, it's a complex question to answer. But overall I believe it was
somewhat easier for Müller; yes, due to several factors:
1. Müller was an
out-and-out striker, a poacher mainly (but not strictly) <=> Messi is a
false nine, who varies between dropping deep as an extra midfielder or making runs into the box as a poacher
2. the 1972/73 Bundesliga gpg average (3.37) is
0.61 higher than its 2011/12 La Liga equivalent (2.76); not to mention other competitions where the differences are even bigger
3. Barcelona did score
0.26 more goals per game than Bayern did; however this is also impacted by the aforementioned league gpg averages, which would indicate that Barcelona should theoretically have scored even more goals in a league with 0.61 more goals per game on average
4. both players play in a perfectly suited environment that they had been accustomed to for at least 7-8 years; both teams have many contemporary greats, but Müller had a
genuine all-time great in Beckenbauer (often seen as TOP10, sometimes TOP5) with whom he would often engage in 1-2s. Messi has Xavi (maybe at most TOP25 all-time?) and Iniesta (surely outside the TOP50).
5. stylistically, I don't think there's that much of an advantage to either player: Barcelona
dominate possession and thus have many more opportunities, although this past season they have been repeatedly frustrated by very defensive tactics (parked busses) <=> Bayern's games were far
more open, with more space for attacking players to operate in.
Overall, Müller is still a better striker and finisher than Messi IMO, but that just makes it even more incredible that the latter can come close to him in pure goalscoring output!