I have been using EMG 81/60 combo on my Ibanez RG with a full-floating Floyd Rose type tremolo. I am very satisfied with my tone.
Transparency/Flat Output - EMGs are neither totally flat nor too heavily EQ-ed. Depending on the model you choose, they have slightly different voicings, each with their own application.
I am not sure what you meant by needing transparency. If you are talking about tone compression - yes, the EMG clean tones feel slightly compressed but that's something that I like on my clean tone. If it bothers you a lot, you can opt for an easy 18V mod (basically adding an extra battery to the circuit).
EMG 81 has a reduced bass/low-midrange allowing tight tones at high gain and works very well as a high gain rhythm pickup for metal. Say for example the kind of tone you would need for the heavy rhythm part in the ending of One by Metallica. This thing can scream out harmonics with the mildest coaxing...
EMG 85 on the other hand has a boosted midrange and will sound very 'warm' and bluesy. The bottom end can be a little all over the place if you are using very high gain. Clean tones are a little dark but still very pleasant. If you listen to Ozzy, this is the pickup that Zakk Wylde uses for cleans and mild overdrive solos ala the first part of the solo in "Old LA tonight".
EMG 60 is a more flat EQ-ed pickup that sounds fantastic on clean tones and mild overdrive. Very similar to James Hetfield's clean/lead tone in the interlude of 'Master of Puppets' by Metallica.
At the end of the day, tone is subjective to the artist. All the top pickup manufacturers like EMG, DiMarzio, SD etc have a fine range of high quality pickups. When people who categorically classify the entire brand as trash, they usually don't know what they are talking about.
If you think your tone sounds great, it will give you the confidence to play better and hence it will end up sounding better anyway. That's simply because a lot of the sounding good on a guitar also depends on your hands, technique and confidence while playing.
-- My current rig
Guitar: '98 MIJ Ibanez RG520 QS w EMG 81/60
Amp: Laney LC15R Tube, Fernandes 20W SS
Pedals: MI Audio Tube Zone Overdrive, Boss OD3, CS3, MT2, HM2, DS2, CE5, DD7, TU3, Beta Aivin DD2 Delay, Dunlop Crybaby 95Q, Stranger Vol Pedal, BBE SupaCharger
Others: Yamaha RBX 374 Bass, Yamaha MM-6 Synth, M-Audio Fast Track, Shure SM-57, Heet Sound E-Bow Plus
Wanted(pm if selling): EB VPJr/Boss FV500L,Ibanez w Original/Lo-Pro Edge