Seems like if you Google this, you'll come across a fair amount of info on this. A few articles link to Andrew Munn's follow up to his article titled "The Reason Android is Laggy". Andrew summaries a response from Google employee Dianne Hackborn:
...suggest[s] that the increased security and flexibility of the Android platform over iOS is a cause of performance overhead and that increasingly fast hardware will help resolve the issue
Between the two articles, it appears that the lag is simply a performance issue--not a purposefully designed 'feature'.
Just a hunch, but I imagine part of that is due to Google not having direct say about a lot of the hardware Android goes on--combined with the fact that the OS has to support a wide range of devices. A lot of manufacturers want to compete on price and, as such, likely underpower the devices. And since so many devices want to run Android, the OS likely has to make accommodations for scenarios beyond the device you happen to be using.
As for the 'simple tweaking of system variables' I have another hunch that the app mentioned likely also has some trade offs. If it's increasing the performance of one thing, it's likely having to take away from the performance elsewhere.