>>718949959
No.
It was because of an obtuse setting (called "Vsyncs in MTGS Queue") with no real explanation that would inexplicably add 2 frames of delay constantly because it was set to 2. Setting it to 0 would resolve literally all input lag, regardless of what controller or version of Lilypad was used.
The SPU plugins also had unnaturally high latency set by default, backing it off to 10-20ms would also fix that lag.