Mercury is bored today.

The boring method:

Top 5 list of magical girls:

Ami Mizuno and Makoto Kino from SM, Sayaka Miki from PMMM, Fuu Hououji from Magic Knight Rayearth, and Yuri Tsukikage from Heartcatch Precure.

(This actually would make a pretty good team, with Sayaka and Makoto being more combat oriented, Ami and Fuu being strategically oriented, and Yuri somewhere in between)

More interesting methods:

Casting by roles:

Leader: The first thing that popped into my head when I thought of this was Minako Aino from SM. For ones that are actually the protagonist, Hikaru Shidou (Magic Knight Rayearth) or Nozomi Yumehara (YPC5). And now that I think about it, Sayaka Miki would make a pretty good team lead if she was in a show that wasn't PMMM.

Fighter: Hmm... the only ones I can think of right now are Makoto Kino and Haruka Tenou (SM)...

Strategist: See the three mentioned in the boring section.

Emotional Crutch/Cute One: Tsubomi Hanasaki (HPC) was the first name that popped into my head. Madoka Kaname (PMMM) could also work for this category. (most magical girl leads are this, IMHO)

Mentor/Cool One: Rina Touin (Mermaid Melody), also Mami Tomoe (PMMM).

Final team comes out some group of 5 out of all the names above. 

Only using Precures:

Favorite Cure by season:

Moonlight (HPC), Dream (YPC5), Berry (FPC), Ace (DDPC), and Muse (SPC). 

Short version of roles list above:

Leader: Dream or Heart
Fighter: Sunshine or Rosetta
Strategist: Moonlight (this mixed with fighter and mentor)
Emotional Crutch/Cute One: Blossom or Peace. 
Mentor/Cool One: Ace (transformed) 

I told you that I was ridiculously bored...

Well ed won't be going into such detail but she'd go with 

Card Captor Sakura, Sailor Mercury, Robin(Witch Hunter Robin, she's a girl she has magic powers thus she is a magical girl.) Valkyrie for UFO Ultra Maiden Valkyrie, and Serah Farron from Final Fantasy XIII-2. 

I guess your team depends on your definition of Magical Girl. Is it any girl that can use magic or use special powers or does she have to transform into another persona in order to fight? I prefer the former to the later, just due to the fact that i get more magical fun that way. 

But just going off those that must transform in order to use their powers, I would go with 
Sailor Pluto, Sailor Mercury, Princess Tutu, and Sakura. Reason being i like them and i feel that the could make a fun team, maybe not the best fighting team ever but at least it would be fun to watch!

I'm going to choose a team of 5 magical girl idols!

Creamy Mami
Sailor Venus
Onpu Segawa
Magical Star Kanon
Jem

My team of 5 Magical Girls would be:

Leader: Rei Hino/Sailor Mars (Sailor Moon)

Fighter: Scarlet Ohara/Angel Salvia (Wedding Peach)

Strategist: Yuri Tanima/Angel Lily (Wedding Peach)

Emotional Crutch/Cute One: Momoko Hanasaki/Wedding Peach/Angel Peach (Wedding Peach)

Mentor/Cool One: Setsuna Meioh/Sailor Pluto (Sailor Moon)