As someone said above, Gretzky was a very deserving winner of the Hart in '89 based on one player's value to his team, and Mario was also a very deserving (non-)winner based on his being the best player that year and totally dominating his own team.
When we're talking about these 160+ point seasons that only Wayne & Mario have achieved in history, I'm not sure the difference between, say, 168 and 185 points is really significant. Or the difference between 185 and 215. At some point, it's just so far beyond anybody else that it defies comparison. Once you get up to that level of scoring, I think you have to look less at who had more points and more at things like (a) how dominant that player is on his team (Mario would win in '89 based on that criterion) and (b) how much weaker the team would be that season without that one player (maybe Gretzky was a bit more deserving that season).
Maybe another way to look at the 1989 question is: During Gretzky's 1980 through 1987 domination of the Hart Trophy, were there any seasons where, in the literal definition of the award ("most valuable to his team"), someone else should have won?
I personally have issues with giving the Hart to someone whose team misses the playoffs, and apparently voters do also as (as Big Phil pointed out) it's only happened twice in the past 60+ years (the recent one being Mario in '88). One would have to have one of the greatest seasons of all time -- as Mario did in 1988 -- to merit winning the Hart on a non-playoff team (in my opinion).
Anyway, back to my question of Gretzky compared to other potential winner from 1980 to 1987:
1980: Gretzky wins as a rookie. Considering that he powered the Oilers into the playoffs (barely), I think he definitely deserved this. The highest points-per-game as a rookie on a sub-.500 team? Ridiculous.
1981: Gretzky beats Mike Liut... barely! The vote is 43% to 42% for Gretzky. Frankly, that's absurd. I cannot really see how anybody else could possibly deserve the Hart this season, when Wayne got a crappy team into the playoffs and won his team scoring title by 89 points, setting all-time marks for assists and points before he was old enough to shave. It's nuts that it was that close.
1982: Gretzky all the way. 92 goals, 212 points, team-scoring win by 107 points(!). He got 100% of the 1st-place votes for the Hart. (Trottier was in 2nd, with 23% of the votes, but none better than 2nd place.)
1983: Here is the first time where Gretzky might have been legitimately challenged to win the Hart. Not because he didn't totally deserve it, but because of the "competing-with-yourself" rule that the elite athletes are judged by. Anybody else having a 196 point season on the 3rd-best team in the League would be a 100% vote winner, but Gretzky was competing with himself from the previous season, and that leads Hart voters to look elsewhere. 2nd and 3rd-place went to Pete Peeters and Denis Savard, both of whom had worthy-enough seasons, I think. Still, the 1st-place votes were 43 for Gretzky and 14 for Pete Peeters. But Peeters got a lot of votes.
1984: Gretzky deserved it in a landslide. He actually got "only" 55% of the votes despite having the highest PPG in NHL history and scoring 50 goals in 42 games. Rod Langway was 2nd with 18% of the votes.... lol... But anyway, it's a Gretzky landslide.
1985: Gretzky with 53% of the vote. I'm actually surprised he got that much, what with Hawerchuk scoring 130 points and leading Winnipeg to a strong season. Of course, if voters were being objective and not comparing Gretzky to himself, he would surely have gotten 100% of the vote. Anyway, he still got 60 of 63 1st-place votes.
1986: Here's the ultimate example of voters not wanting to vote for Gretzky, despite the overwhelming evidence. Yes, he won the Hart, but with "only" 52% of the vote, in a season when he scored more points than any player in history and led his team to 1st-place overall. Lemieux was 2nd, with 30% of the votes, despite his team missing the playoffs and Gretzky outscoring him by 74 points. Gretzky still got 54 of 60 1st-place votes, though.
1987: Gretzky with 52% of the vote. 2nd-place is Ray Bourque with 20%. Gretzky gets 49 of 54 1st-place votes.
Given this precedent of the 80s, it's both surprising and not surprising that Lemieux didn't win in 1989, but I don't think it's unprecedented (as I'll mention below). It's surprising in the sense that all of Gretzky's wins (except 1980) were in seasons where he had total offensive statistical dominance, as Lemieux did (or didn't...? see below) in '89. But on the other hand, the voting record shows that in two seasons when Gretzky had far more statistical dominance than Lemieux in 1989, a fairly large percentage of voters didn't vote for him! This occurred in 1981 (he barely won the Hart, which is nuts) and in 1983 (he won fairly easily, but Pete Peeters got lots of votes).
About the precedents: Previous to all this, in 1976, Montreal had a better season than Philly and Lafleur outscored Clarke by 6 points, but the Hart went to Clarke. Likewise in 1975, Clarke was 4th in scoring but won the Hart. Bobby Orr was quite clearly (I think) the best player in the NHL all season and set records for a defenceman of goals and points in a season, and outscored Clarke by almost 20 points, and yet Clarke won the Hart. Again, in 1973, Clarke is 3rd in scoring but wins the Hart. In 1971 and 1972, Orr was 2nd in scoring but wins the Hart (though no one would argue with those). 1965, Bobby Hull is 4th in scoring but wins the Hart.
So, clearly it is not unprecedented for one forward to win the Hart who is beaten in scoring by another forward.
But it is rare, if not unprecedented, for a forward to win the scoring title by as much as Lemieux did in 1989 (31 points) and not win.
But here's the catch: When Gretzky was winning in 1982, 1983, 1984, 1985, 1986, and 1987, he was outscoring the 2nd-best scorer in the League by at least 70+ points EVERY YEAR. (The exception is 1981, when he outscored #2 by "only" 29 points... but broke all-time records for assists and points in doing it.)
These seasons contrast with Lemieux in 1989, who, despite a fairly easy Art Ross win, beat the 2nd-best scorer by "only" 31 points. Nor did Lemieux break any single-season records in doing so.
What I'm suggesting, then, is that winning a scoring title by 75 points is different from winning a scoring title by 31 points, regardless of the raw points scored.
I think once a player (and they are only Gretzky or Lemieux) gets up to 160+ points, the absolute number of points becomes a bit unimportant in assessing importance to your team. The difference here is that when Gretzky reached (and far surpassed) those levels, nobody else was anywhere close to him. But when Lemieux achieved those levels in 1988 and 1989, Gretzky (and even Yzerman and Nicholls in 1989 somewhat) was close to him. At that point, I think it is justifiable for voters to look beyond who was the best scorer and focus more on who was more impactful on his team that season.