As my title states, I'm going to show you all my idea of how certain events should have played ou. or at least how i would have done it. I'm mostly going to be using characters that were misused (i.e Big Tiny, Allen, Martinez). So:

Season 3.

3x01 Plays out as shown.

3x02 Group encounters prisoners. Big Tiny is not killed. Rick does not kill Tomas, he instead decides to imprison him until he decides how to handle the situation. Andrew meets same fate as originally shown. Other prisoners are exiled

3x03 Plays out as shown. Dr.Stevens is replaced by Dr.Sub

3x04 Andrew begins to sabotage the prison as he did previously. Lori still dies dies during childbirth. T-Dog is not killed. Andrew frees Tomas during the chaos. Carol is confronted by Andrew within the tombs but manages to knock Andrew into walkers who proceed to devour him allowing Carol to escape with her bandana still falling. Prisoners are recruited. Big Tiny, Axel and Glenn part. Oscar and Rick are confronted by Tomas in the same fashion as Andrew. Oscar kills Tomas.

3x05 Plays out as shown. Development for new characters

3x06 Plays out as shown. Development for new characters

3x07 Big Tiny is recruited as well. Plays out as shown. Development for new characters

3x08 Tyreese's group arrives at the prison. Donna is not bitten but she sustains injury that hinders the group. Shootout plays out, but Oscar is injured instead of killed. Big Tiny is killed. Daryl is still captured. Governor bears slightly more severe beating by Michonne.

3x09 Battered group rescues Daryl and Merle. Daryl and Merle depart. Tyreese's group+ Donna are forced to leave prison.

3x10 Axel and Carol bond. T-Dog takes Axel's death. Axel cowers in fear and Carol instead hides behind T-Dogs corpse. Axel's cowardice reflects badly with Carol straining their relationship. Rest of episode plays out as normal.

3x11 Plays out as shown. Return of Daryl makes for more story with Axel and Carol. Recent loss of T-Dog+ introduction of Merle makes for conflict. Development for new characters. 

3x12 Plays out as shown. Development for new characters

3x13 Plays out as shown. Development for new characters

3x14 Donna stays at Woodbury as Martinez+others leave to walker pits. Rest of episode plays out as shown.

3x15 Axel agrees to accompany Michonne and Merle. Merle knocks out Axel and Michonne taking only Michonne. Donna is killed in shootout with Merle and Ben is injured. "mean woodbury guard is not killed"

3x16 Mounrful Allen stays back and tends to sons wounds. "Mean Woodbury guard is killed by the Governor instead of Allen. Episode plays out as is until Rick reaches Woodbury. Upon entering Woodbury group is confronted by Allen. Allen is knocked out by Tyreese in order to subdue him. Milton is killed but Andrea survives. Woodbury survivors join Prison.(+Dr.S, Allen, Ben,Sasha, Tyreese, Karen)

Season 4

4x01 Allen is still shown to be mourning the loss of his wife and shows extreme fear of losing Ben, Andrea attempts to console him by attempting to relate to him by how the Governor hurt alot of people, but this exasberates their relationship. Michonne comments on how he has every right to be upset after what the Governor did, Andrea questions Michonne's reasonings behind still looking for him. Axel is shown to be helping Rick with the farming. Big Lot scavenging group now includes Axel, who has stepped up in order to make up for his previous cowardice. He is now  valued member of group. Zach is killed. Rick's arc remains the same. Patrick turns.

4x02 Cell block D is attacked by the infected. Rescue group is joined by Oscar, Allen, Andrea. Ben is rescued by his father. Mika and Lizzie are still orphaned. Cell block is cleared Axel, Oscar and Andrea aid the others as the walkers assault the fences. Rest of the episode plays out as shown with Karen and David being killed. 

4x03 As flu begins to spread Sasha, Glenn, Dr.S, Allen, and Oscar begin to show symptoms. Andrea accompanies scavenger group

4x04 Episode plays out as is.

4x05 Dr.S warns Hershel of terminal patients and that he must be prepared to lose some. Refers to a terminally ill Oscar who asks "How do I look?" taking the place of Dr.S. Ben, Carl and Beth protect the elderly and young. Rick and Carl deal with alkers.Outbreak occurs exactly as shown except Oscar turns instead of Dr.S with Dr.S merely being unconscious. Julio attempts to help Hershel but is subdued by a walker.Oscar is put down and Hershel manages to contain the threat. Scavenging group returns and all the infected are given antibiotics.

4x06 Plays out as is.

4X07 Martinez is not killed but is merely scared into following the Governors will, convinces him that he is unfit. Group decides to rid themselves of Pete as he is deemed "Dead weight" by his inability to kill. Rest of episode plays out as shown. 

4x08 Ben and Allen are seen embracing due to Allens recovery. Axel grieves over his friends death. Governor appears with both Hershel and Michonne. Andrea, Axel, Allen, Ben, Maggie, Beth, Bob, Daryl, Sasha, Glenn Tyreese, Michonne, Carl, Julio and Dr.S appear on the courtyard while Rick negotiates with the Governor. Group prepares for battle. Allen and Ben share a moment similiar to Hershel and Billy's in the comics. Hershel is executed. Emergency plans are enacted by Rick's group. battle commences. Axel is the first casualty. Michonne escapes and retrieves her sword.Meghan is killed and is put down by the Governor who orders the tank to demolish the fences. Dr. S accompanies Beth as she searches for Judith. Allen and Ben are pinned down. Beth and Dr. S find Judith and attempt to flee. Dr.S stay behind to buy Beth time. Dr. S is shot and is mortaly wounded. Andrea assists Bob and Sasha in defending. Allen and Ben attempt to make their way towards Andrea, Stookey, and Sasha, but Ben is killed in the process breaking Allens will to continue fighting. Allen is executed by Alisha. Glenn is evacuated by the bus. Julio is killed. Tyreese is pursued by Alisha and others but is saved by Lizzie and Mika. Lizzie and Mika leave with Tyreese. Beth and Judith are killed by a tank shell. Maggie is forced to to leave with Andrea, Stookey, and Sasha as Stookey is injured and the Governors militia is advancing. Daryl is pinned down by enemy forces and is bitten in then process by a walker. Kills various soldiers with a grenade and destroys tank. Daryl then kills Mitch but is confronted by Martinez. Martinez is killed but Daryl is left mortally wounded and slowly begins to die. Michonne rescues Rick and mortally wounds the Governor leaving him to be killed by Lilly. Rick and Carl find the corpses of both Beth and Judith but are forced to leave.

Final death count for the prison battle:









Dr.S =8

In my opinion, this death count would have been much more satisfactory than just the death of Hershel( and Julio). I'm sure they writers would have been able to write much more interesting subplots and roles for the characters than I was able to to. This was mostly written on the fly. Comments and questions are welcomed.