Arkhon - I think the biggest surprise to me for my deck was correctly reading the reaction people would have to seeing Shaper. I know Anthony/Anthony take a cautious approach, heavily icing R&D, then scoring when it'll leave them in a good position afterward. From snooping around BGG and talking to other players, it seemed like people thought rushing agendas against Shaper was the correct move (not saying one is right or one is wrong, Shaper with a full rig is a tough cookie to deal with). This is especially true when you're under the gun to score, and have 65 minutes for a match. I exploited this by making a deck that encouraged rushing by having an incomplete rig, then having surprise access through tools like Tinkering, Inside Job, TR/Femme, Test Run, Stimhack, etc. Also TR/Sneakdoor took everyone off guard, which was great. You could improve this with an HQ Interface I suppose, but I didn't find it necessary.
My biggest surprise was how little Weyland I saw. It definitely had a presence, but like on OCTGN, what was top dog back in the day is just another identity. HB FA was by far the most common deck played by the more experienced players, and should probably be the archetype you want to build against for your runner deck. Andromeda was the most common and (hard to judge, given their outsized presence) most effective runner, which surprised me a bit -- I think I prefer playing Gabe, but someone stole my Underworld Contacts so I haven't been playing Andromeda much, haha.
Shobalk - I agree that Indexing isn't better than R&DI for all decks. If you have a solid economy, and R&DI can allow you sustained accesses every few turns you're probably better off with that since you may get far more accesses. The goal of this deck is to use tools to allow cheap access to areas while looking poor. Tinkering was very helpful for an early Indexing, since it's usually just an Enigma, Katana, Roto, Wall, etc covering R&D and may set you back 4-6 credits. TR/Femme is also very useful for defense like Tollbooth.
That being said, you expect to see 2 agenda points in 5 cards, so you're highest likelihood is to flat out score an agenda if you can access twice. The next most likely scenario is to see no agendas, and after that pulling multiple agendas. Paying 5-10 credits to have the expectancy of 2 agenda points seems pretty good to me! Also R&DI has a discount with Kate that I wasn't getting.
I absolutely agree that Indexing loses steam once R&D gets well defended, but so do all R&D access cards. My thought was that as long as I had access, I better make it pay off, especially since I have cards that can substantially reduce the cost of access, like Tinkering, Inside Job, Stimhack, etc. Also Maker's Eye pairs very well with it, and I found myself hanging on to them until I could Index. If I played R&DI the corp could prep for it, and the economy in this deck just can't afford that. If I were running MO it'd be different, but I'm not a fan of it for a variety of reasons.
It's not that Indexing is a miracle card -- it just got lost in the R&DI hype (a powerful card in its own right). There's a human fallacy where when we see two similar things, we tend to like the "better" one more than we should and dismiss the "worse" option. I think that's what happened to a lot of people when they saw Indexing and R&DI. Remember the reaction to Marked Accounts vs PAD Campaign?