The tournament format that most emphasizes winning is single-elimination. I mean, literally: if you don't win, you're out.
The problem with single-elimination is that it the order of elimination doesn't necessary tell you something about a player's overall achievement. Assuming the tournament winner is legitimately the "best" player, we really can't say who is "second best" based on tournament standing alone. If the winner's first-round opponent was actually the most difficult match, maybe he or she is really the "second best" player, despite getting out immediately. So you'll know who's first but everyone else's place in the standings is kind of a crapshoot.
The single-elimination format is also rather frustrating for high-variance games (I would say Settlers is one), and being knocked out early can be very dissatisfying for tournament participants.
Most Swiss systems do emphasize winning, in the sense that they're literally counting wins as the main scoring system. One pitfall in Straight-Swiss is that it's possible for a player to functionally win the tournament before getting to the last game -- this is similar to what happens when one player scores 3-0 in a "best of five" match. A popular way to avert this is a "Top N," where top-scoring players from the Swiss rounds come together for a single-elimination bracket.
Top N has the benefit of making sure the top players are actually pitted against each other, and the single-elimination part of the format does promote a heated final where everyone is playing to win. However, this actually encourages what you've called "brokering third game deals" in the last rounds of the Swiss -- if I can get into the Top 16 with a third-place finish in my last Swiss game, for instance, there is no reason to play for the top.
As best as I can tell, the Swiss system will always produce some irrelevant matches and predetermined outcomes. The best you can do is to tweak where those occur in the tournament structure. Top N is a compromise that keeps those features out of the finals, at the cost of filling the final round before finals with a series of tricky forfeits and draws.
It's my opinion that it's better to accept "brokered" draws (with a prohibition on bribery and collusion to keep the game fair) than to try to force people to play irrelevant games. What you can do to discourage intentional draws and forfeits, however, is to associate an incentive with your overall ranking going into the Top N. In current Magic: the Gathering tournament rules, for example, Top 8 games give the higher-ranked player the ability to choose his or her position in the turn order (instead of deciding randomly, as they do in the preceding Swiss rounds).
I think the 5-3-2-1 structure you've cited is, in general, a good example of a Swiss-style format that emphasizes winning over second-place finishes and promotes a reasonable level of competition in the final Swiss round before Top N.
For starters, first is disproportionately more valuable than the other results: a first-place finish and a last-place finish are worth as much as two second-place finishes; and finishing first, second, and third is worth more than finishing second three games in a row.
Note also the role of wins in tie-breakers:
1) Top overall score [of three rounds of Swiss] (15 being max)
2) Most 1st place wins
3) Top winning margin (Ex: a game ends 10-7-7-6, thus the winner has a
+3 margin; All margins are summed)
4) Win in game 1
5) Win in game 2
6) Win in game 3
7) Highest dice roll -- 2D6
Here the margin of victory is used only as a tiebreaker, as an attempt to factor in the decisiveness of wins if players are tied for quantity of wins.
Finally, this bit is important:
Playoff rounds will be seated by rank (see below) but the game format will be the same
Tournament Playoff Round:
Once the top 16 players are set, seating will be done according to the following chart:
Table 1 - #1,5,9,13
Table 2 - #2,6,10,14
Table 3 - #3,7,11,15
Table 4 - #4,8,12,16
So, there is some incentive to finishing the Swiss rounds with the highest rank possible: you can get a leg up in the turn order (I'm assuming the tournament organizers consider this an advantage in Settlers).
That said, because I don't consider going first to be always preferable in Settlers, I'd do something like this instead: "After the board is laid out, players at the final tables get to choose their seats in rank order." A little bit of extra privilege (and strategic depth) for placing first!