
I've gone back and looked at the the last 3 seasons. I chose 2005 as a starting point because it was the first year of the Clavijo era and because the only player remaining with the team from prior to that is Pablo Mastroeni. Since in 2005 and 2006 MLS played a 32 game season I've added columns for points, goals, and goals against per game.

The Rapids finished right in the middle of the pack in the Clavijo era in points. They had a better offense than ever before, but the second worst defense. Overall the Rapids had their 5th worst season, ahead of 1997, 2007, 1996, and 2001 at .88 points/game being the worst. Out of those 5 years only in 1997 did the Rapids make the playoffs.
Looking at the team position by position:
Goalkeepers: Bouna finished the season as the #1 keeper, a position he never should have lost. Burpo was a serviceable backup for a mid-season pickup that was forced on us when Justin Hughes went down with a season ending injury right before Bouna left for Senegal. He should have never been named the starter though, and our defense suffered in the last third of the season because of it.
If Hughes can come back from injury we should cut Burpo loose. Bouna is out of contract and is rumored to be heading to Europe. The Rapids should do everything they can to re-sign him, and if they are unsuccessful they'll need to find a new keeper either to start or to back up Hughes if the coaches have enough faith in him.
Defenders: The back line was constantly shuffled under Clavijo, but came together under Smith. The back 4 of Kimura, Petke, Gibbs, and Harvey did fairly well with the exception of a run of 3 games where 10 goals were conceded. I think Kimura and Harvey are locks to start out wide next season, but the Rapids need to look for help int he center of defense. Petke implied to fans after the last game that this was it for him as a player, plus he's out of contract. Gibbs was inconsistent at times, and will head for Europe if any team gives him a chance. Ihemelu and Erpen are good for at least one mistake a game each, and while that might be OK if you have strong veteran presence in your back line, counting on them to be the veterans will just lead to disaster.
In a best case scenario the Rapids keep Gibbs and pick of a solid central defender with Ugo as a back up. If Gibbs leaves we'll have to do some serious scouting for defenders or consider switching to a 3-man backline.
Midfield: The big question mark in midfield is Christian Gomez. The Rapids can't afford to not play their highest priced player that cost them a DP slot, but Smith didn't seem particularly interested in using him. Gomez has expressed his displeasure in interviews as well, so there's some work to be done there if Gomez is going to play for the Rapids again. Pablo is also expected to leave for Europe after possibly his best season as a Rapid. Losing him will be a blow to the team. A good season from Nick LaBrocca softens the blow somewhat, but LaBrocca is at best a decent MLS player, he's not a top level National Team player like Pablo is. Cooke and Clark seem locked in on the wings, Clark will need to work on being more consistent next season, at times he seemed to disappear from games this season.
If Gomez works out his issues with Smith and/or a new coach and Pablo doesn't move to Europe our midfield is set. If we lose both of them LaBrocca will slide in to Pablo's spot and we'll have to go looking for another playmaker. The Rapids currently have nobody on the roster that can run the offense from the center other than Gomez. The Rapids did so well in the late half of the season by using the wings but with no real threat in the center that won't sustain the Rapids for a whole season.
Forwards: Conor Casey exploded over the last 5 games of the season, notching 6 goals. He's clearly become the best forward on the team, but I think he's actually over-rated after his late season run. That's not to say he couldn't be the centerpoint of our offense in 2009, but I think the Rapids should try to strike while the iron is hot and see if we can get a steal in a trade. If we can't though, the offense in 2009 should be geared towards Casey. McManus and Cummings spend the season trying to claim the starting spot next to Casey. They both bring different skills to the table. McManus brings the grit and passion, along with being a threat from anywhere within 35 yards. Cummings brings speed and determination, but needs to work on his finishing.
I think that either Cummings or McManus could start next season, with the other being a super sub off the bench. It just depends on what kind of style the coach wants to play. Casey would be the other starter if not traded. The Rapids need to look for depth at striker, the only other forward on the roster is Jacob Peterson. They would do best by finding somebody that has a good chance of being a MLS starter to put pressure on McManus and Cummings to step up to the next level. If Casey is traded they'll need another guaranteed starting striker as well.
Bench/Reserves: The Rapids have a very experienced set of bench players and reserves to draw from. Jacob Peterson, Ugo Ihemelu, Facundo Erpen, Stephen Keel, John DiRaimondo, Mehdi Ballouchy, and Jose Burciaga all got significant playing time this season. While I think some of those players are best to let go, it still gives the Rapids some maneuvering room.
Ihemelu, Keel, and DiRaimondo all look like they are ready to take the next step and become starters/regular subs either for the Rapids or another MLS team through a trade. The Rapids need to look for depth at keeper and forward in the offseason. Midfield and defensive depth appears to be covered.
Coaching: Well, Clavijo is gone and the team played better under Smith. Then again I'm pretty sure a pet rock could have gotten the team to play better than they did under Clavijo. Most of the decisions the Rapids have to make that I've discussed already hinge on who the coach will be and what kind of soccer he wants the team to play. If its Smith then the Rapids should probably plan on not having Bouna or Gomez and focus on playing a defensive game to rack up 1 goal wins. If its John Spencer the Rapids will probably open up more and try to dominate other teams (Based on Spencer's attitude and Houston's style of play). Until a decision is made though, the rest of the offseason is just a big mystery.
Overall the Rapids had another mediocre year where they finished no better than 3rd, just like every other season in their history. When the Rapids replaced Mooch Myrick with Tim Hankinson after the 1999 season the reason given was that AEG didn't think Mooch could take the team to the next level and win a championship. As history as shown, only Mooch Myrick has been able to get the Rapids to a championship game, and nobody has been able to finish in the top 2 in the conference. Picking the right coach is the biggest decision the Rapids organization has had to make since KSE took over. They failed the first time with Clavijo, if they fail again they may not recover for years.