Sure, it seems out of place given knowledge of the highway history, but that old chestnut about the 90s restructuring being so very disruptive is not backed up empirically.
I would say that fact is, at best, debatable.
Okay, lets go through it then.

Apparently the numbers were off in my first post. The actual segments:
75 segments had the numbering retained as is:
Numbering maintained:
2 Tilbury to Hamilton
2 Hamilton-Toronto (no numbering applied, but was unassumed and known by names to begin with)
2 Toronto to Ganaoque
2 Gananoque to Lancaster
2A
3 Port Colborne
3 Fort Erie
4 north of Clinton
4 south of Talbotville
5 west of Peters Cors.
5 east of Clappisons Cors.
6 south of Port Dover
7 Brampton to Markham
8 Kitchener-Cambridge
8 Hamilton
12 Durham
14
15 south of 401
19 south of Tillsonburg
20
22
24 south of Simcoe
24A
25 south of Acton
25 north of Grand Valley
27 south of Barrie
27 north of Midhurst
28 south of Peterborough
29
31
32
33
34
36
38
41
42
43
45
46
48 northern segment
49
50
52
55
56
59 south of Courtland
62 Maynooth to Barrys Bay
73
74
76
78
79
80
81
83
84
86 west of Elmira
87
88
89
90
91
92
93
95
96
99
117
118
121 south of Haliburton
136
169 south leg
169 north leg
420
39 segments in which the route was renumbered to provide greater route continuity:
QEW Gardiner transition at more logical point, a major interchange
3 Leamington to Wheatley incorporated into local road network
6 Alvanley to Hepworth incorporated into county network
7 west of Thedford renumbered to provide clearer navigation CR-22 E-W, CR-79 N-S
7 rerouted to better bypass Peterborough
7A renumbered to provide proper through route for Hwy 7
15 Carleton Place to Arnprior - Complete numerical consistency within section isolated from other, reversion to earlier number
16 416 to central Ottawa consistent number for isolated segment
16 renumbered to Hwy 416 with freeway upgrades
17 now 174 in Ottawa
18 fully incorporated into municipal network
19 Ingersoll to St. Marys isolated route number is continuous
19 Stratford to Tralee incorporated into county network
21 south of 401 incorporated into county network, transition at major junction (Hwy 401)
23 highway rerouted, old segment incorporated into sequential CR system
24 Paris to Brantford rerouted onto more appropriate through route
24 Shelburne to Collingwood consistent number for isolated segment
25 isolated segment between Acton and Ospringe has consistent number
25 portion between Brisbane and Waldemar incorporated into RR-24 through route
28 Peterborough to Lakefield bypassed segment given new consistent number
35A incorporated into county network
40 south of 401 incorporated into county network, transition at major junction (Hwy 401)
44 extension of RR-49
51 incorporated into longer CR-15
54 N-S portion incorporated into through route of CR-18, E-W portion to Cayuga has consistent number
62 Complete numerical consistency within section isolated from other
65 rerouted onto more direct route
69 renumbered to Hwy 400 with freeway upgrade
70 renumbered to provide proper through route for Hwy 6
86 renumbered to provide greater continuity with regional network, reversion to earlier number of Hwy 85
115 highway rerouted, bypassed segment reverted to municipal names, Hwy 115 ends at more logical point (freeway end)
121 Fenlon Falls to Minden, Now CR-21, so number is somewhat retained, isolated from unrelated section
121 Haliburton to Hwy 28, incorporated into Hwy 118 through route
131 incorporated into CR-27, a more direct routing
133 incorporated into longer CR-4
134 - renumbered to provide proper through route for Hwy 28
148 numerical consistency with county road
14 segments with numerical discontinuity:
2 Windsor to Tilbury - numerical discontinuity at Essex-CK line
3 Leamington bypass incorporated into local road network, through movement turns from E-W to N-S
3 Leamington to Talbotville - numerical discontinuity at Essex-CK line
7 numerical discontinuity at Halton-Peel line
9 Western segment connects into CR-109, proposal to renumber to Hwy 109 was rejected by local governments
11 numerical discontinuity at York-Simcoe line
17 numerical discontinuity at Ottawa-P&R line
47 numerical discontinuity at York-Durham line
53 numerical discontinuity at Oxford-Brant line
58 Welland segment goes into RR-54
67 south of Hwy 11 is named road
24 numerical discontinuity at Waterloo-Wellington line
24 numerical discontinuity at Wellington-Peel line
59 numerical discontinuity at Oxford-Perth line
That being said, 4 of those 14 are where the highway goes from xx to 1xx which isnt rocket surgery to figure out. Additionally, there is very little through traffic at Tilbury (Hwy 2) and on Wheatley (Hwy 3). The balance of that, is yes, a little shaky. But not unmanageable.
And yes, this does omit B-routes, which are deliberately avoided due to concerns with 911 dispatch, and secondary highways that were transferred because I didnt feel like going into those (though by and large they retained their numbers too).
Again, the vast majority of segments that were transferred either retained their numbers, or had their numbers changed to provide greater consistency. Sure, its harder to follow the old route of a road like Highway 25 without changing numbers, but the reason it was changed was that there wasnt demand to do that.