Don't think Shapiro ever claimed or promised they would build a great farm system. His comment about "waves of prospects" can be interpreted differently. Every decent MLB team needs a consistent pipeline but that doesn't mean they ever need an elite farm system, necessarily. There are a number of consistently successful teams that rarely have great farm systems.
Shapiro's criticism of AA was mostly based on the over-aggressive path to building that led to the required rebuild from 2017 on. I think Atkins and Shapiro believe Toronto has the resources to never need to enter a full rebuild.
Say what you want about the last few years, which have of course had disappointing results on the whole, but they have avoided horrible long term commitments while remaining competitive. Springer's deal is up after 2026, and Berrios' deal while it runs through 2028 is not bad at all considering his 2023 resurgence and his age (not old!). Gausman is a big asset right now on his contract.
Lot of focus on the Vlad/Bo window but even if these guys walk, that just means that Toronto will have like $42.5M in freed up payroll space after 2025 to court a huge free agent or two. Also, Bassitt ($22M), Green ($10.5M), IKF ($7.5M), Romano (Arb3), Mayza and Swanson are off the books after 2025 if not extended, so lots of money will be freed up. Also Turner and Kikuchi and KK and Yimi and Jansen and Richards ($47M) freed up after this season, we will see how much of that is recommitted in 2025 to arb raises and free agents.
Teams go down the tubes when they have sandbag commitments or dead money, and a s***** farm. Toronto has a middling farm system right now but the financial outlook at the MLB level is pretty solid, IMO, in a long term sense. So if they keep spending money intelligently, year over year, there aren't a lot of worries.
The farm system could tread water, Vlad and Bo could walk after 2025, and Toronto could still compete in 2026. It's a distinct possibility. One big free agent replaces Bo... a waiver claim 1B replaces Vladdy based on his 2023 performance.
Actually developing some elite prospect talent would certainly help take the team from an 88-92 win team to that 98+ win team everybody wants, though.