There are, of course, several problems at work here. If it is the case that HS2 could be doing better in terms of biodiversity - and I'm not questioning that point, just acknowledging that some don't believe it - then there are several sources of that.
One of the things to bear in mind is that the transport secretary was, for three wholly unwelcome and infuriating years to those of us in the transport sector, Christopher Stephen Grayling. He's a f.cking idiot. You don't need me to tell you that. But if you've never had to see the impact of his being secretary of state for the area that you have some good knowledge and experience in, it's quite hard to understand just how sh.t he is/was.
I've told this story before, but it's worth re-emphasising to try to get across the purity and strength of his closed-mindedness and idiocy. Some of the work I and my team do contributes to understanding the whole life costs of different options for investment in the railway. In track, one of the big innovations is under-sleeper pads
. They're not exactly advanced tech - they are literally just foam pads attached to the underside of concrete sleepers (the preferred sleeper type on the railway), which cushions the interface between sleeper and ballast, and reduces the forces transferred to the ballast. Over time, ballast - the stones used to support railway sleepers - wear down from the repeated force of trains passing over them, and reduce in size. This leads to uneven compaction and that, in turn, can cause various other issues including corrugation of the rails. Certain refurbishments may be done, and actions such as tamping or stoneblowing can help. Eventually, though, the ballast needs renewing. This requires closure of the railway, typically booked years in advance, and is a job which is extremely heavy on materials, plant and labour. It's expensive. Under-sleeper pads hugely extend the lifetime of the ballast between renewals, by about 40%, for an up-front spend of around 2% extra. From a whole life cost perspective, they're an absolute no-brainer, so much so that they're now required by policy in Network Rail.
East West Rail, however, isn't internal to Network Rail (despite several NR staff working on the project development) - it's a separate company. As part of the specification of the reinstatement of the line, under-sleeper pads were recommended as being required on the basis of whole life cost. During "value engineering" workshops, however, which are basically just excuses for lowering the spend regardless of impact*, the pads were removed from the spec on the say of Grayling himself, because they cost extra money. 40% extra life of the track up in smoke, because of his stupidity. EWR have made other terrible decisions, such as not electrifying from the start**. But nonetheless, hopefully you can see the impact that these stupid decisions have on how things go.
Grayling was, unfortunately, SoS for much of the key period of the development of the specification for HS2. Despite them having the enormous budget they do, they are looking at every point for how to avoid spending too much money. Naturally, this doesn't extend to the number of directors they have or the compensation they pay to their contractors, and HS2 have got a good team looking at whole life cost-based decision making for the infrastructure itself (led by someone from our team). But when it comes to things like cycle lanes or meeting biodiversity commitments which lie outside of the assets directly managed by the company, those are the sort of "green crap" areas where Grayling would have been pushing them to cut costs. HS2 and Network Rail have had, shall we say, "discussions" around issues such as interfaces between the two railways, and particularly EWR alignment north of Aylesbury. HS2 are trying their best to transfer as much of the cost out of their own project as possible. It makes sense, but doesn't always fly.
None of this is trying to excuse anything, just to explain. A £100bn budget is, of course, absolutely enormous. But be aware that hidden within that budget are some often furiously energetic discussions about how far that stretches and what HS2 can avoid doing - discussions encouraged, of course, by the government, who would rather it didn't cost £100bn, but a lot less.
*see the Grenfell Tower Inquiry for more details
**a decision which Grant f.cking Shapps has recently supported, because oooh big shiny battery trains. Network Rail's decarbonisation strategy will see all but the most uneconomic 10% of the railway electrified, which will eventually include EWR. Grant Shapps is a moron.