Introduction
This article introduces the Comprehensive DPS model. The model takes into account of:
 Energy gains from damage
 Energy waste from overcharge
 Edge cut off damage from fainting
when calculating a Pokemon's true DPS. Basing on Felix's work, this author has improved the model and applied it in various case studies:
Notation
We are given two input variables:
 $x$: the energy left of the Pokemon when the battle ends
 $y$: the DPS of the enemy
And the following parameters from the Game Master file or calculated by the damage formula:
 $FDmg$: the Damage per use of the fast move
 $CDmg$: the Damage per use of the charge move
 $FE$: the Energy gained per use of the fast move, positive
 $CE$: the Energy used per use of the charge move, positive
 $FDur$: the Duration of the fast move in seconds
 $CDur$: the Duration of the charge move in seconds
 $CDWS$: the Damage Window Start of the charge move in seconds
 $Def$: the current Defense stat of the subject Pokemon
 $HP$: the effective HP of the subject Pokemon
Our metrics of interest are:
 $FDPS$: the DPS of a fast move, which equals to $\frac { FDmg }{ FDur } $
 $FEPS$: the EPS of a fast move, which equals to $\frac { FE }{ FDur } $
 $CDPS$: the DPS of a charge move, which equals to $\frac { CDmg }{ CDur } $
 $CEPS$: the EPS of a charge move, which equals to $\frac { CE }{ CDur } $
 $DPS_{0}$: the Simple Cycle DPS
 $DPS$: the Comprehensive DPS
Formula
DPS Theory
Derivation
Define:
 $n$: the total number of fast moves used by the Pokemon in the battle
 $m$: the total number of charge moves used by the Pokemon in the battle
 $T$: the duration of the battle
The first equation is the Time Equation :
$$ n \cdot FDur + m \cdot CDur = T $$The second equation is the Energy Equation :
$$ n \cdot FE + 0.5 HP = m \cdot CE + x $$Note: for onebar charge moves, to account for overcharge, we adjust $CE$ by treating it as if it requires more energy to fire. The overcharge energy could result from either fast move overcharging (on average $0.5 FE$) or losing the energy from damage before your energy gets used (at $CDWS$):
$$ CE = CE + 0.5 FE + 0.5 y \cdot CDWS $$Note2: The above formula is to be improved, though.
Then we solve the above linear system for $n$ and $m$:
$$ n = \frac { T \cdot CE + CDur \cdot (x  0.5 HP) }{ FDur \cdot CE + CDur \cdot FE } $$ $$ m = \frac { T \cdot FE  FDur \cdot (x  0.5 HP) }{ FDur \cdot CE + CDur \cdot FE } $$Last but not least:
$$ T = \frac { HP }{ y } $$Finally, by the definition of DPS (total damage over time):
$$ DPS = \frac { n \cdot FDmg + m \cdot CDmg } { T } $$ $$ = ... $$ $$ = DPS_{0} + \frac{ CDPS  FDPS } { CEPS + FEPS } \cdot (0.5  \frac{ x }{ HP }) \cdot y $$Comprehensive DPS Axiom
The Comprehensive DPS Axiom is the following statement:
Comprehensive DPS must be no less than the Fast Move DPS and no greater than the Charge Move DPS.
In mathematical expression, it is:
$$ FDPS \le DPS \le CDPS $$The Domain
The Comprehensive DPS Axiom can imply the domain of $DPS(x,y)$ as a function of $x$ and $y$. Recall that
$$ DPS(x, y) = DPS_{0} + \frac{ CDPS  FDPS } { CEPS + FEPS } \cdot (0.5  \frac{ x }{ HP }) \cdot y $$For simplicity, define
$$ z = (0.5  \frac{ x }{ HP }) \cdot y $$Then the Comprehensive DPS formula can be rewritten in the Weighted Average Form:
$$ DPS = \frac{ FDPS \cdot (CEPS  z) + CDPS \cdot (FEPS + z) } { CEPS + FEPS } $$The Weighted Average Form suggests that $DPS$ is the weighted average of $FDPS$ and $CDPS$ with the weights of $(CEPS  z)$ and $(FEPS + z)$ respectively. To satisfy the Comprehensive DPS Axiom, both weights must be nonnegative:
$$ CEPS  z \ge 0 $$ $$ FEPS + z \ge 0 $$which is then
$$ FEPS \le z \le CEPS $$This is the domain of $z$. In terms of $x$ and $y$, it is just $$ FEPS \le (0.5  \frac{ x }{ HP }) \cdot y \le CEPS $$
Along with the nonnegative nature of $x$ and $y$: $x \ge 0, y \ge 0$, the domain of the $DPS(x,y)$ is defined.
Relationship with Simple Cycle DPS
How does the Comprehensive DPS introduced in this article ($DPS$) relate to the traditional Simple Cycle DPS ($DPS_{0}$)? Recall that:
$$ DPS = DPS_{0} + \frac{ CDPS  FDPS } { CEPS + FEPS } \cdot (0.5  \frac{ x }{ HP }) \cdot y $$Therefore, Comprehensive DPS is a generalization of Simple Cycle DPS. It can be expressed as a range while changing $x$ and $y$. Some important implications:
 When $y = 0$ (i.e., there's no damage from enemy; the battle lasts infinitely long), $DPS = DPS_{0}$.
 Another case where $DPS = DPS_{0}$ is $$ 0.5  \frac{ x }{ HP } = 0 $$ or, $ x = 0.5 HP $. This means that the total wasted energy ($x$) exactly cancels out the total energy gained from taking damage ($0.5HP$), resulting the DPS the same as if there was no damage taken  which is just the Simple Cycle DPS.
 The term $$ \frac{ CDPS  FDPS } { CEPS + FEPS } $$ is seen in some other DPS models which also consider energy from taking damage. We may name this term "Energy Efficiency" and denote it as $EE$. From the Comprehensive DPS Axiom, $CDPS > FDPS$, therefore $EE > 0$.

Since $y > 0$ and $EE > 0$, whether $DPS$ is greater than $DPS_{0}$ only depends on the sign of $ (0.5 HP  x) $:
 When $x > 0.5 HP $ (i.e., there is more wasted energy than the total energy from damage), $DPS < DPS_{0}$
 When $x < 0.5 HP $ (i.e., there is less wasted energy than the total energy from damage), $DPS > DPS_{0}$
Application
DPS Spreadsheet
When making a DPS spreadsheet, we want to compute the average value of $DPS(x,y)$ when $x$ and $y$ take different values. Assuming $x$ and $y$ are independent and all other terms don't depend on $x$ or $y$, We have:
$$ E[DPS(x,y)] = E[DPS_{0} + \frac{ CDPS  FDPS } { CEPS + FEPS } \cdot (0.5  \frac{ x }{ HP }) \cdot y] $$ $$ = DPS_{0} + \frac{ CDPS  FDPS } { CEPS + FEPS } \cdot (0.5  \frac{ E[x] }{ HP }) \cdot E[y] $$ $$ = DPS(E[x], E[y]) $$Note: For multibar moves, "all other terms don't depend on $x$ or $y$" holds. For onebar moves, however, since we apply punishment to $CE$, $CEPS$ depends on $y$. That said, the relative error is minimal. We will use the formula $E[DPS(x,y)] = DPS(E[x], E[y])$ for both onebar and multibar moves.
Then the next question is to find $E[x]$ and $E[y]$. Basing on empirical simulation data, the following formulas are used in a neutral settings:
$$ \begin{cases} E[x] = 0.5 CE + 0.5 FE \\ E[y] = \frac { 900 } { Def } \end{cases} $$In a more specific setting (when the enemy is specified), some more sophisticated formulas are used:
$$ \begin{cases} E[x] = 0.5 CE + 0.5 FE + 0.5 \frac{ \lambda \cdot FDmg_{enemy} + CDmg_{enemy} } { \lambda + 1 } \\ E[y] = \frac{ \lambda \cdot FDmg_{enemy} + CDmg_{enemy} } { \lambda \cdot (FDur_{enemy} + 2) + CDur_{enemy} + 2 } \end{cases} $$where:
 $\lambda = 3$ if the enemy has onebar charge move
 $\lambda = 1.5$ if the enemy has twobar charge move
 $\lambda = 1$ if the enemy has threebar charge move