I think I've been able to determine that Thomson has some definite practices. Most of them seem designed to increase player confidence / development. If you think about it - you'll be able to see most of them in his managerial style. My interpretations for the reasons for some of them could be wrong - but I think these are the rules. I'd be interested in your comments if you think I'm wrong or I missed some significant distinctive practices.
This is not a rant. He has been very successful with these rules.
1) Not playing is never punishment - there is no "benching you for that". There is a logical reason for sitting a player that doesn't have to do with their personal performance. I don't know whether Thomson felt hurt by this as a player or he is just that much a "player's manager" but it is a priority rule. I think Thomson may put a player in more who is hot, but not at the direct expense of another player if possible.
2) Relievers are mostly taking one inning "mini-starts". He wants pitchers to finish innings if possible. In this way they can feel they "did their job" even if they gave up the go-ahead, etc. He may look at which hitters are coming up and handedness when selecting a reliever - but he plans the bullpen usage around relievers coming in at the top of the inning and pitching the inning (and often a different reliever coming in for the next one). This is not inviolate - he does bring relievers in during the inning occasionally - but he is slow with the hook. Compared to some other managers, relievers don't often pitch multiple innings (there are exceptions - Turnbull, etc..) This may be somewhat inspired by beginning his managing in the "3 batter faced rule" era.
3) A corollary to #2 is that he wants starting pitchers to try and finish every inning they start and go back to the dugout getting the final out. Again - very slow with the hook. He wants starters - even if they've given up the lead, to get out of their current problems on their own if possible. I think this rule is less strong than rule #2 - but it is there. He is trying to guess with every starter whether they have another whole inning in them - because he doesn't like pulling starters in the middle of an inning.
4) Pitcher's platoon splits stats matter - hitter's don't. He will bench LH hitters against pitchers "tough on LH hitters" - even if they have statistically a reverse platoon split. And he does the same with right handed batters. The platoon split stat for the pitcher is believed. The platoon split stat for the hitter (whether it is reverse or negligible) - is not. He will stack the lineup with LHBs against RHPs and visa versa. Especially if the stats indicate a strong split for the pitcher.
5) Everybody plays. The roster (13 players each side) is small in Thomson's eyes and he is going to play everyone. If someone hasn't played in three or four days he is looking for an opportunity to get them in - no matter whether they are a backup shortstop or last seat bullpen pitcher. He doesn't want players just sitting on the bench or in the bullpen because they "aren't needed" or "only a spare". This is harder to do for catchers (see rule #10) because they can only be used as catchers - but it does happen through rule #7. This was a practice of Whitey Herzog too.
6) There is a caste system. Young players - however hot they are or however well they play - need more decisions made for them than seven eight figure salary veterans. In fact eight figure salary veterans, "stars" should have a good bit of say in how they play. Thomson is a player's manager - not an authoritarian. 7 figure veterans (Cave, Merrifield) don't have as much say as 8 figure veteran stars.
7) Most players will get occasional rest days. Players will often get a rest day every week or two - especially if there is no team rest/travel day. This helps with rule #5 (everybody plays). Thomson seems less likely to bench a struggling player for rest out of concern it will be interpreted as "benching" (rule #1). The starting catcher needs more rest than most players and Thomson will try and rest Realmuto one day/game a week or more even if there is a travel day. "Stars" may not rest if they don't want to - because rule #6 trumps rule #7.
8) The batting order doesn't matter so much - you might as well make players happy with it. Schwarber likes hitting 1st, Harper likes hitting 3rd. You might as well let them. On this I agree with Thomson - there are not good statistical studies indicating that batting order matters that much (as much as fans scream about them) you might as well make players happy. Thomson doesn't move players up and down to punish them. Thomson will try to alternate or at least not have three batters of the same handedness in a row - because with the three batter rule - it makes selecting relievers easy for the other team when there are strong streaks of handedness in the batting order. I think when you have a Harper type elite hitter - it does matter to get a good hitter behind him so he isn't just walked.
9) Thomson is more likely to use a pinch runner than a defensive replacement. If the game is a runaway he may "rest" veteran players by replacing them with bench players, but only if it is a complete runaway (like 10 runs). He almost never puts a better defensive player in with a narrow lead to try and protect the lead. This may again be due to not wanting to communicate "mistrust" of a player's defensive ability. For some reason this does not extend to baserunning. If the game is close and a runner gets on - he sometimes will replace a slow runner with a faster one.
10) There must always be a backup catcher on the bench in case the catcher is injured. Like Girardi - Thomson fears running out of catchers he won't use a catcher from the bench in any way that might put him in the situation of not having a backup catcher on the bench. Even though the roster is small - it is smaller for catchers. If the backup catcher - Stubbs - is starting - Realmuto will not be used as a pinch hitter (or runner) or to play first base. Even though this rule is near last in this list - it is actually a very strong rule.
11) The season - getting into the playoffs - matters more than any single regular season game. Thomson does try to focus on winning the "next game" but is unlikely to make decisions in the starting lineup / starting pitching or during the game that characterize any regular season game (before the last several weeks) as a "can't lose game". He doesn't want to burn relievers if he doesn't have to or replace players in game because another player is hotter. He might replace a hitter for a lefty/righty matchup reason - but there will be a reason - not just "your bat is cold". Player development can happen during the season and is worth doing (although he has said he doesn't want pitchers trying new pitches during the season). Some of spring training can bleed over into the early season. Thomson is patient and plays the long game across the whole season. Thomson does change his stance on this in the late season and playoffs and can change to a more ruthless every pitch, every at bat, every inning, every game matters approach.
12) Weather doesn't matter. We've seen the Phillies play in a lot of foul weather (by baseball standards) and Thomson doesn't seem to have different practices for bad weather. He doesn't sub players to avoid injury or play a lot more conservatively. It's still baseball even when it is swampball.
Some rules are frustrating for Phans. Players say (for example) "Merrifield is worthless - why would Thomson ever play him?!" but there is rule #5 - everyone plays. Until Dombrowski/Fuld take a player away - Thomson will play him. The same goes for pitchers. It matters what circumstances players are played in - but Thomson will use every player. Castellanos will never be "benched" - Dombrowski/Fuld will have to take Casty away or Thomson will continue to play him. Some Phans have big problems with the batting order. They will ask - "why would you let Rojas bat there when he's so cold?!". In May Thomson will have Rojas hit in his turn even in late innings with the game on the line, in October - he'll pinch hit for him if he can.
Again, I think there is some good thinking in much of this. Thomson is a smart career baseball man who is not ruled by stats. His record certainly endorses these practices.
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