the first reason i used Scenes when it became available was to cut down on the number of presets i used for "very similar" sounds.
on the Ultra, i used 5 presets regularly. for the most part, they all had the exact same blocks, set exactly the same.
P1 - Clean, no effects
P2 - Clean, add chorus and quiet delay
P3 - Clean, add volume boost, turn off chorus, longer louder delay
P4 - Distortion, rhythm tone
P5 - Distortion, lead tone, add delay
for simplicity of organization, i had the same additional effects (phaser, rotary, etc) in all 5 presets, mostly because at the time, foot controllers could not change buttons per preset.
P1 - P3 were exactly the same, except different blocks were turned on and off. and if i needed to change the Amp block in P1, guess what... i had to go to P2 and P3 to change it as well. P4 and P5 used different amp blocks, but all else was the same except for blocks on/off as well.
this was typical of how most modelers worked back then, with things completely separate. with real pedals, i would have to press multiple pedals each time i wanted to change sounds, rather than just pressing ONE button. for me, this is the main appeal of digital gear - one button to change multiple things, and also that my settings are saved without risk of knocking a knob during transport or setup.
enter the Axe-Fx II. i got it when it launched, and it did NOT launch with Scenes - that came in FW9 i believe. but the Axe2 did have GLOBAL BLOCKS. this let us link blocks to some "template" and among presets where blocks were linked, a change in one Preset changed all linked blocks. this helped to keep things organized and make your sound the same among your different Presets.
but i still had the same 5 preset setup, and all 5 presets were still doing basically the same thing, but just turning things on or off, with really only the Amp block switching.
then Scenes appeared in FW9. and then i could use ONE preset. since my 5 preset setup was basically all the same blocks, this worked perfectly as Scenes can turn blocks on/off and change XY state of the block. so instead of hopping around 5 presets, i stayed in one, and just used Scenes.
what is the technical advantage? maybe none, really, since i was changing Amp types, i didn't get the seamless switching - but i really don't need it, since i got used to changing sounds with a Mesa Roadster which also didn't have seamless channel switching. but it helped my organization since i knew exactly what effects were in the preset and their settings - i was just turning things on and off, like you would a pedalboard of real effects. there weren't any surprises.
because a preset CAN change everything, sometimes you may forget that you changed this, or added that, and whoops, i thought i had a quiet sound on that preset....
i think Scenes are great. but i also think it depends on the complexity of your presets and sounds. there are many people using the Axe-Fx - with all of its advanced functions - the same way one would use a processor from the 90s. and that's ok! 1 preset per sound, very few blocks, very little real-time control of parameters. just like a 1-to-1 sort of deal. again, that's totally ok.
it depends on how you can visualize and organize your sound, rig, and setup. for some, losing the visual cue of the real pedals in front of you is a huge, huge change. and some who have been using the Axe and MFC for years now still aren't completely comfortable with not having the dials of all the pedals in front of them. some people just want to SEE that the phaser rate is set to 1 o clock on the dial, even if they never need to change it - they just want to see it there before they turn on the phaser.
while i do think that mentality should change now in 2018, old habits die hard. it's funny - i know die hard analog guys who have purposefully shunned anything digital all these years of guitar playing. with Digitech and Line 6 bringing affordable modeling and digital effects into real popularity in the 90s (Boss was always there, but didn't cause the surge the others did), they didn't try anything at all - "it sounds digital" i was told. and sure, a real tube amp that you've been playing for 30 years is something you're just used to.
but then the Axe came along and for the first time... there was something... but they still ignored the standard and the ultra, and tried to ignore the Axe2. but with the later FW of the Axe2 their interest got piqued. they just had to try it. and for many, yup, it was close. exact for them? maybe not. but close enough. suddenly that 50 pound amp with their 20 pound pedal board just didn't seem as appealing as a 14 pound rack case... so they tried it. and they liked it. but again, the habitual things were gone - messing with the pedal board connections before the gig, adjusting knobs on pedals - not because you had to, but because it's just what you do. seeing all the knobs while you play, you know, just to make sure they're still set the way you want. and much more.
i digress.
Scenes are an option. if Presets work for you, use them. i use Scenes heavily. for the last 6 years, i've basically used ONE preset at every gig. sometimes it's a different preset per band/gig, but it's typically just one. i know what options i've given myself in that preset, and i've setup scenes for different sounds/options within that preset. and i give myself a few switches to turn on effects that aren't programmed in scenes. it's easy to remember during the gig, i have a wealth of tone options, and i'm NOT changing everything (presets) during the show and accidentally using the wrong sound.
here's a video (i used to charge for this) i made a while ago which explained the history of Presets, XY and Scenes. it's always good to know how/why a feature developed as it helps you determine when/why to use it: