On a cheerier note, to summarise the trip:
Irkutsk / Lake Baikal is a great place to visit with lots of things to see and do, with the emphasis being on the natural world. I chose a week because the direct flight to/from HKG only runs weekly and it turned out to be a good length of time, but you could do longer. If you go all that way you should do more than Lake Baikal.
Weather is critical to a good experience. The best weather is July and August. That of course coincides with peak numbers but given that most of the attractions are natural and its a 'big' scenery place, that isn't the issue that it would be in, say a city of museums and churches. We were so lucky with the weather on this trip - it could have been cold and windy the whole time which would have greatly detracted from the trip. But the autumn colours were a major part of the experience on this trip.
Winter is another 'high season' period, where driving on the frozen Lake Baikal, ice fishing, ice cave visits are the go. I want to return to do this next time.
There is more to do in the region than I did. The 'circum Baikal railway' is a complete misnomer but people like it very much. Its a day trip from and return to Irkutsk where you take an electric then steam train on part of the original TSR rail tracks around the SE corner of the lake. I would have loved to do the Trans Siberian Railway from Beijing to Irkutsk - its 2 full days and nights.
S7 is an airline I'd be happy to use again. Both my 5 hour flights in J were serviceable without being spectacular. I'd be happy to do them from Irkutsk to the west of Russia, I think, depending on the plane config.
Tourist facilities outside of Irkutsk are below the standard you'd like BUT you could definitely do better than I experienced with a bit of forewarning (here) and planning. As I mentioned up-thread, there is a hotel in Khuzhir on Olkhon Island and certainly better hotels in Arshan than we got there. I don't know why I didn't quiz the tour company as to the quality of accommodation provided - I just assumed too much, I think. But if you plan to go in peak season, you'd have to book well ahead to get the good places. With a bit or warning, we could have substantially self-catered out of Irkusk on the Tunka Valley tour.
I used 'Baikal Secrets' tour company but I'm not sure there would be much difference between the various tour companies you' find on trip Advisor, as they all seem to use freelancers to actually run the tours EXCEPT I know Ivan of Baikal Secrets runs the winter ice tour himself and maybe others as time permits.
The Courtyard Marriott in Irkutsk was a very good choice. They were very helpful in supplying me with the 'invitation' needed for my Visa and in that process, and at the hotel, their English was good. There are several other hotels that looked good as well - CM rated about #5 on Trip Advisor.
There are some really good restaurants in Irkutsk, with an emphasis on fresh fish from Lake Baikal.
Getting a Russian Visa is a laborious process, but there is plenty of help here on AFF if you need it. Apply as early as possible - I think the earliest you can apply is 3 months prior to your arrival date. Certainly the experience you get makes the application process worthwhile.
The couple who joined me on the Tunka Valley tour have convinced me to go back, and see the area around Novosibirsk/Tomsk in central Siberia, so going to Europe next time may be on S7 via Irkutsk, Novosibirsk and St Petersburg!